I seem to remember in one of the games or on the wiki that said the Enclave virus doesn't affect people in vault.

This could possibly mean that the Enclave could recruit these people into there army. Giving a small "excuse" for the weird amount of soldiers around.

Also in fallout 2 sergeant Dornan & the purple guy say they are expecting recruits. This could be referring to people from vaults or just some of the Enclave citizens.

Only in Fallout 3 where the virus was some-how immune to pre-war humans, in Fallout 2 the virus just killed and required an innoculation.

The recruits in FO2 were all coming from the rig. I remember one scientist saying so. (about 2 days ago)

The oil rig had a secret Vault built in. along with it's advanced manufacturing facilities. The Enclaves plans for the vaults (The control ones atleast) was for post cleansing re-population to the best of my knowledge.

Wouldn't the people in vaults be safe though? Because of the fact there in a vault?

I do not think so most the other vaults were expendable or worse they would get forced opened and labor camped or killed being well in not Enclave approved heh so to speak.

It's a virus so I don't know, they could be killed if they left, not enough details are known about it. It was described as a "Bio-chemical weapon."

The Vault-Tec Vaults? A most assured No.

Anyone "Worth Saving" was in an Enclave facility. Anyone not... Isn't worth bothering with.