Diminished numbers of Enclave? We say way to many in Fallout 3. Navarro did not have that many people. Some stayed and fought NCR, others gave up, which means only a fraction of the small number at Navarro went East.
Well that's unconstructive; clearly then if that doesn't explain the numbers then it can't be right. Here's a new idea, when the reactor alarm went off all of the Vertibirds at the ENCLAVE evacuated with as many people as possible. Let's assume that in preparation for the Project that the numbers at Navarro were increased as to prepare them for life on the mainland. Next let's assume that
after the ENCLAVE was destroyed, hardly anybody left for a multitude of perfectly valid reasons:
1. Arcade was born in 2246 and even his childhood memories of Vertibirds, energy weapons and even exact quotes. So that what, 2249 at the most conservative estimate? Clearly there was some leadership and structure there.
2. Navarro must, therefore, have been self-sustaining.
3. It is a highly defensable fortress, according to the Enclave Communications Officer, "What are you talking about, your on the coast you have great defenses."
4. According the
President Richardson himself, "It'd certainly paint me a picture of what life's like in that radioactive hell on the mainland." Therefore, we can assume that the government and the citizens largely unaware of mainland affairs.
5. Clearly even people who "Hated what the Enclave was doing" stayed at Navarro because of ties to people, the need to survive; even going by your "Everyone at Navarro deserted" idea then surely what would
actually be more beneficial and easier would be if everyone stayed at Navarro out of a Powder Ganger like necessatey.