Those Enclave people may have been defeated but there is no solid proof that there are not 100,000 men just outside the boarders of the map. Enclave can surface when ever the writers want them to where ever they want them to. Because no one knows for sure.
No they won't. They were a small branch of ex-government officials and military personnel, that thought they were above the others. They only saved the people that they thought would be important to their cause. There was never many of them, if there had been it wouldn't have been a shadow government.
And Enclave has been taken down twice by people who barely knew how to use weapons when they started their quests. It's probably true that Enclave could take down the NCR and the legion in Mojave, but in reality NCR is much stronger than they seem to be in Mojave. They are a full blown nation, not some remnants of the past with a impressive storage of pre-war weapons. NCR has a lot more production than Enclave could ever dream of having with their fascist übermensch mentality. Gunrunners have the means to produce energy weapons for NCR, but they don't ship them to Mojave because they always got raided. Basically even if Enclave was able to rise against the NCR and they would be eventually cut down by militia and guerrilla warfare by NCR.