In Kings and Numbers, the pot of manna and Aaron's rod are never stated to be in the ark. The pot - tsintseneth - is mentioned once as 'before' the testimony, as is the rod - matteh. Moses later took the rod to strike the rock, after which there is no more mention of it. The ark itself is never seen again after Jeremiah's single mention. This is designed to prevent any kind of superstitious attachment to the artefacts. This enables faith to grasp the spiritualities of that which is signified. And when the statements in Hebrews are seen as having a spiritual meaning regarding God's tabernacling - how 'He dwells between the cherubim' - then we see the writer's emphasis is on God's dwelling, not the fabric of the tent. That being so, then the items mentioned previously are not in the ark - not in the 'it' which is finally mentioned.
Here is an explanation of this, beginning with comment on Hebrews 5:12. The readers:
"...needed to be taught again the elements of the beginning of the
oracles of God. If they needed to be taught again, then this was not
mere legal instruction for that they had received from their
I believe it is clear from the scriptures I have mentioned that, in
the Oracle, was the ark but without a mention of the kapporeth or
the kerubim which were part of that kapporeth. Instead we have the
kothereth and we have the constructed kerubim which are not made of pure gold - as were the original kerubim of the kapporeth - but
were olive wood overlaid with gold.
But the writer of Kings specifically mentions the fact that within the
ark were the stone tablets. The entire Oracle, and its surrounding
building, is to be seen, I believe, as a concept which encapsulates
all that the ark of the testimony conveyed, but the Oracle also
conveys more. There are palm trees on the walls - the kaph of God.
His handprints are everywhere. There are kerubim also. Everywhere is
fruitfulness, and flowering. It is a place of life and spiritual
activity. It is a place of Divine purpose.
In this Oracle, it is - almost - as if the ark is open. As though that
which it, figuratively, contained - is risen. He is not here. But
there are kerubim. And they are olive wood. 'I am like a green olive
tree in the house of God,' saith David, Psalm 52:8. And here, the Lord
speaks to David. Thus David does not descend to the pit.
Here, it [is] as though the tables of stone are in plain sight, but
there is no plague... they are contained. There is kaphar. And
because there is kaphar, there is helios, composure. And because
there is contained composure, there is steadfast strength.
This is the reason that the writer to the Hebrews almost states - but
not quite - that three items were in the ark. But if one looks further
one sees that his view is more spiritual than the mere artefacts that
were constructed. He sees tables, rod, and pot under one
overshadowing, is my perception. He sees the place where God dwells;
he is not looking at the fabric of the tent or the wooden box. And
such is his perception that his words almost - but not quite - imply
material facts that could not, at the time, be so stated in material
demonstration. Then, he deliberately says no more. It is John the
Apostle who shall be more particular, later. About four decades later,
to be precise.
Here, hilasterion, will God meet with men. Here in the place of
containment and resolution. Here where, justly, there is uplifting and
unburdening. Here, above the kapporeth - and the kothereth. Here,
between the kerubim. For here is God composed. Here - and here only -
does he see that which is a contradiction but, seeing it, he passes
by, for it has been - absolutely - contained." The Cherubim of
Glory, pp85-87 & 182, Nigel Johnstone, 2015 (Bold mine)
Why is there such attention paid to literal objects in questions about the Ark when the objects are but signs signifying spiritual realities, which it is vital that people of faith grasp? I do wonder. As the writer above concudes:
"For the cherubim in the Oracle are not solid gold as were they
carried in testimony through the wilderness. The carried testimony is
one thing; that which grows in the house of God is another. And there
is the olive tree, as it were, inside the cherubim, for they are olive
wood overlaid with gold. It is as though the olive tree grows up
inside the cherubim. That which grows up from the earth, as a tree,
grows into the cherubim. Growing in the house of God, in the anointing
of the oil, shall one grow to realise and fulfil, in Christ, what
cherubim represent." (Ibid. p131)