In Dawnguard, I have found an interesting tidbit. If you talk to Dexion before getting the Dragon Elder Scroll, you can ask him about it, and he says that all the Elder Scrolls in the Imperial City vanished in 4E175 and were scattered around Tamriel by forces unknown. 175 was the year the Great War ended. As we all know, there are no such thing as coincidences. So, why did the Elder Scrolls vanish?

Because the devs want us to find an Elder Scroll (or three) in every DLC.

Because at long freakin' last, the titular plot coupons are prominently featuring in critical main-line quests.

The greatest accomplishment of the Mede dynasty: Sending the known Elder Scrolls away into hiding before they could be seized by the Dominion.

[/maybe?]

Protection measure against Dominion control of the city.

The elder scrolls have a mind of their own like rare artifacts. They probably sensed that after the great war, someone will need to find them again, so they moved their locations accordingly. You didn't find any of the imperial city ones, because two of them were with vampires since before the great war, and the dragon one was in a dwemer ruin for hundreds if not thousands of years.