Now the matter of geography. Groom Lake, NV is about fifty miles NNW of North Las Vegas. Nipton is about half that distance to the south, and the Utah border is about that same distance to the East.
True that leads to a point, Nellis AFB was hit as Groom Lake Facility would suffer the same fate considering those are high value targets, Nipton would be very low on the list.
Since House did not save Nellis that is pretty much on his backyard then it would be even more unlikely he could do anything to save Groom Lake Facility or even have a reason to do so.
The Fallout Universe is very loosely based upon the real world, and you all should try to remember that before you start getting upset at each other.
On Area 51 defense, the Fallout universe diverges in the 50's and Groom Lake Facility was re-activated (Groom Lake served for bombing and artillery practice during WWII) in 1955 for the U-2 project, chances it did existed in Fallout universe.
However the connection of Area 51 with Aliens come later, with the OXCART program (SR-71) since it had a unusual airframe and the later Have Blue project (F-117) certainly helped with that idea also due to being a aircraft with a unusual airframe.
Actually a lot of bases in Nevada are pretty old .. Nellis and Groom Lake origins date back to WWII, Dugway Proving Ground in Utah also dates back to WWII ... divergence is more about places like Tonopah Army Air Field that closed down at the end of WWII might still be operational in Fallout Universe, you have a good example of that with Nipton were it prospered in Fallout Universe when in the world we live on, its a very small place with a population of 20.