When creating your own work, you can always decide that a high-priority asset like a military base was preserved by reasons besides secrecy and "dummy" installations:
Defensive systems - After the ABM treaty between the US and the USSR, each side was allowed a fixed anti-ballistic-missile capability. The Soviets deployed their system around Moscow. The US deployed theirs in the Midwest to protect (some) missile silos (btw that's real-world, not FO history). The prewar US in Fallout would have wanted to build some kind of defensive systems, and used them to protect leadership, military, and economic targets over the population. The various energy weapons developed right before the war are a good example. The first weapons of this type would probably be large and stationary, needing a big power source.
Partial destruction - even a high-priority target, if it's large (like the Nellis-Tonopah-Test Site is) likely has many discrete targets, and needs to be hit with multiple warheads. Some warheads don't go off or never arrive.
In the 1991 Gulf War, the US could try to bomb something, wait a couple of days for cloud cover to dissipate, check out the site by satellite or air, find that the target wasn't hit, and have to hit it again. Sometimes, even a third time or more. That was that "high-tech videogame war with smart bombs" that some of us may recall. Read the official history here, but only if you are a total geek:
http://www.airforcehistory.hq.af.mil/Publications/Annotations/gwaps.htm
Now imagine a two-hour all-out nuclear war. No time for BDA (bomb damage assessment) or re-attacking a target. You just fire it all, probably hitting targets multiple times (this could account for the level of destruction implied by Fallout). Even so, some targets would escape destruction. However, in the example of a large military base, the overall area would appear destroyed to anyone trying to go there, and be highly radioactive.
Remember that the whole complex that Area 51 is in is larger than many US states (and several European countries). There's lots of room for something to escape the bombs.
Whew. Time for a nap.