What are the physical, archeological and scientific historical supports that the Vatican used to suppress her status as a saint in 1961?
On May 24, 1802, in the Catacombs of Priscilla on the Via Salaria Nova, an inscribed loculus (space hollowed out of the rock) was found, and on the following day it was carefully examined and opened. The loculus was closed with three terracotta tiles, on which was the following inscription: lumena paxte cumfi. It was and is generally accepted that the tiles had not been positioned in the sequence of the words, and that the inscription originally read, with the leftmost tile placed on the right: pax tecum Filumena ("Peace with you, Philomena"). Within the loculus was found the skeleton of a female between thirteen and fifteen years old. Embedded in the cement was a small glass phial with vestiges of what was taken to be blood. In accordance with the assumptions of the time, the remains were taken to be those of a virgin martyr named Philomena. Her name means 'daughter of light'. Philomena is the patron saint of infants, babies, and youth. - St. Philomena (Wikipedia)
Archeological basis and people who oppose
The belief that such vials were signs of the grave of a martyr was still held in 1863, when a December 10 decree of the Sacred Congregation of Rites confirmed a decree of April 10, 1668. But this view has been rejected in practice since the investigations of Giovanni Battista De Rossi (1822–1894).
The questions were raised in particular by Orazio Marucchi, whose conclusions won the support of Johann Peter Kirsch, an archaeologist and ecclesiastical historian who is the author of the article on Philomena in the Catholic Encyclopedia,
Who is Orazio Marucchi?
Orazio Marucchi (1852 - January 1931, Rome) was an Italian archaeologist and author of the Manual of Christian Archaeology. He served as Professor of Christian Archaeology at the University of Rome and director of the Christian and Egyptian museums at the Vatican Museums. He was also a member of the Pontifical Commission of Sacred Archaeology and was a scrittore of the Vatican Library.
And what are the findings of Peter Kirsch?
The inscription on the three tiles that had provided the Latin name "Filumena" ("Philomena" in English) belonged to the middle or second half of the second century, while the body that had been found was of the fourth century, when the persecutions of Christians had ended. Not only the name but also the leaf, the two anchors and the palm that decorated the three tiles, and which had been believed to indicate that Filumena was a martyr (though the necessary connection between these symbols and martyrdom has been denied), had no relation to the person whose remains were found.
Kirsch, Johann Peter. "St. Philomena." The Catholic Encyclopedia. Vol. 12. New York: Robert Appleton Company, 1911. 29 Apr. 2013 - St. Philomena (Wikipedia)
Problems with the question of the OP
The Vatican in 1961 did not suppress the status of St. Philomena as a Saint.
The Vatican in 1961 did not suppress the cult of St. Philomena.
The Vatican thru the Congregation of Rites in 1961 published the Congregation's decision in Acta Apostolicae Sedis "ordered the feast of St. Philomena Virgin-Maryr to be expunged from all liturgical calendars. The Congregation's did not order to suppress St. Philomena's status as a saint and the did not order to suppress any devotion to Her cult that a Supreme Pontiff had clearly proclaimed.
To know more about Acta Apostolicae Sedis here is some pertinent information;
Acta Apostolicae Sedis (Latin for "Register of the Apostolic See"), often cited as AAS, is the official gazette of the Holy See, appearing about twelve times a year. It was established by Pope Pius X on 29 September 1908 with the decree Promulgandi Pontificias Constitutiones, and publication began in January 1909. It contains all the principal decrees, encyclical letters, decisions of Roman congregations, and notices of ecclesiastical appointments. The laws contained in it are to be considered promulgated when published, and effective three months from date of issue, unless a shorter or longer time is specified in the law.
The AAS also contain the "decisions of the Roman congregation". The Latin text cited was a decision not by Pope St. John XXIII but by the Congregation of Rites only.
Is the Congregation of Rites decisions superior over the decision or declaration of the Supreme Pontiff? The answer is No. The Pope is the Supreme Interpreter, Legislator and Guarantor of Faith and not the Congregation of Rites.
The Latin text cited above and published in Acta Apostolicae Sedis was a decision coming only from the Congregation of Rites and does not bear the decision or the prudential judgement or even the approval of Pope St. John XXIII. In contrast to the Congregation of Rites in the year 1837 where the decision of the Prefect of the Congregation of Rites bears the approval of Pope Gregory XVI.
In 1837, the Prefect of Congregation of Rites publicly asserted that Pope Gregory XVI had approved the Congregation's decision permitting the local recitation of the Office,and celebration of the Mass of the Virgin-Martyr, in honor of Philomena in August 11. - Source
Here, we can see the force of authority of the Congregation of Rites issued in Acta Apostolicae Sedis has been put into question because it does not bear the approval of Pope St.John XXIII that had cause confusions among the faithfuls in the year they issued the Congregation's decision in 1961.
In fact, when one of the faithful who had a deep devotion to St. Philomena asked St.Pope Paul VI about the issues & confusions sorroundings the Congregation's decision, simply said "Just don't mind it, continue your devotion".
St. Pius X declaration raising the cult of St. Philomena to Universal Archconfraternity cannot be alter by any future Popes much more by a mere Congregation of Rites decision.
The Confraternity of Saint Philomena was raised to the rank of Archconfraternity by Pope Leo XIII, November, 1886
On June 16th, 1907, the Supreme Pontiff Pius X, receiving in audience Father Petit, from Paris, the director of the Work of Saint Philomena, exclaimed: "Ah, Saint Philomena! It is very sad to read what has been written recently against her" (The Holy Father was referring to certain detractors of the cult of Saint Philomena who dared to maintain that our Little Saint did not even exist.) "It is incredible," continued the Holy Father, "that such things can come about without them (the detractors) looking at the great argument in favor of the saint, the Holy CurÉ of Ars. By her, in her name, and through her intercession, he obtained innumerable graces and continual prodigies."
To definitively affirm the cult of Saint Philomena and to give the final word, on May 21, 1912, Pope Pius raised the Venerable Archconfraternity of Saint Philomena into the Universal Archconfraternity with the Apostolic Brief, "Pias Fidelium Societates," in which he states very clearly: "We decree with the present words that it shall remain always stable, valid and effective, that it receive and obtain its effects fully and completely, in this way it must be regularly judged and defined, and if it proceeds in any other way, it will be null and without value, whatever the authority might be…" - The History of the Universal Archconfraternity of Saint Philomena
St. Pius X had made a decree in May 21, 1912 with a very clear statement that no future decision can alter the decision they had made raising the cult of St.Philomena to Universal Archconfraternity.
Did the Congregation of Rites in 1961 oppose this decree of St.Pius X? The answer is No.
or the better question is;
Can the Congregation of Rites has a canonical power to oppose the Decree made by St. Pius X in May 21, 1912?
The clear answer is NO. Therefore, the devotion to the Cult of St. Philomena stays and the status of St. Philomena as a saint remain because the Congregation of Rites in 1961 cannot also oppose the Congregation of Rites decision in 1837 to celebrate the Office and offering of the Mass in honor of St. Philomena Virgin Martyr because it has the expressed public approval of Pope Gregory XVI, while the latter has none.