Has a Pope ever encouraged, such as in an official letter or audience, separated spouses to strive toward reunion?
The Catechism of the Catholic Church (CCC), issued by Pope John Paul II, says that reunion is the ideal that should be sought, if that is possible:
Yet there are some situations in which living together becomes practically impossible for a variety of reasons. In such cases the Church permits the physical separation of the couple and their living apart. The spouses do not cease to be husband and wife before God and so are not free to contract a new union. In this difficult situation, the best solution would be, if possible, reconciliation. The Christian community is called to help these persons live out their situation in a Christian manner and in fidelity to their marriage bond which remains indissoluble (No. 1649).
Moreover the Code of Canon Law (CIC) says
Can. 1151 Spouses have the duty and right to preserve conjugal living unless a legitimate cause excuses them.
Can. 1153 §1. If either of the spouses causes grave mental or physical danger to the other spouse or to the offspring or otherwise renders common life too difficult, that spouse gives the other a legitimate cause for leaving, either by decree of the local ordinary or even on his or her own authority if there is danger in delay.
§2. In all cases, when the cause for the separation ceases, conjugal living must be restored unless ecclesiastical authority has established otherwise.
Can. 1155 The innocent spouse laudably can readmit the other spouse to conjugal life; in this case the innocent spouse renounces the right to separate.
Hence, yes, the Church does encourage couples to reconcile, if that is possible. (That does not mean, of course, that the Church encourages victims of abuse to remain in abusive relationships; there are many other reasons why separation might occur.)
The Catechism of the Council of Trent encourages separated spouses to reunite:
Advantages Of Indissolubility
Lest, however, the law of Matrimony should seem too severe on account of its absolute indissolubility, the advantages of this indissolubility should be pointed out.
The first (beneficial consequence) is that men are given to understand that in entering Matrimony virtue and congeniality of disposition are to be preferred to wealth or beauty a circumstance that cannot but prove of the very highest advantage to the interests of society at large.
In the second place, if marriage could be dissolved by divorce, married persons would hardly ever be without causes of disunion, which would be daily supplied by the old enemy of peace and purity; while, on the contrary, now that the faithful must remember that even though separated as to bed and board, they remain none the less bound by the bond of marriage with no hope of marrying another, they are by this very fact rendered less prone to strife and discord. And even if it sometimes happens that husband and wife become separated, and are unable to bear the want of their partnership any longer, they are easily reconciled by friends and return to their common life.
The pastor should not here omit the salutary admonition of St. Augustine who, to convince the faithful that they should not consider it a hardship to receive back the wife they have put away for adultery, provided she repents of her crime, observes: Why should not the Christian husband receive back his wife when the Church receives her? And why should not the wife pardon her adulterous but penitent husband when Christ has already pardoned him? True it is that Scripture calls him foolish who keepeth an adulteress ; but the meaning refers to her who refuses to repent of her crime and quit the disgraceful course she has entered on.
From all this it will be clear that Christian marriage is far superior in dignity and perfection to that of Gentiles and Jews.