The Romans taking the Ark in AD70 is one explanation. However, in the bible, the Ark is no longer mentioned after Jeremiah hid it when the Assyrians (or was it the Babylonians) were about to take Jerusalem. 2 Mac 2:5.
So if it was even present in Herod’s temple at the time of Christ is uncertain.
However, when you consider that the Ark was built to contain:
- The Word of God - i.e. the Ten Commandments.
- The staff of Aaron, representing the high priest of Israel.
- Manna - the bread from heaven.
Then…of course, after Jesus came as the Word of God, the new High Priest, and the Bread from Heaven, there was no longer a need for the Ark.
And of course, while Jesus was in her womb, Mary WAS the new ark of the covenant. Also refer to the last verse of Revelation Ch 11, and the first verses of Ch 12.