You can install a mod at any time as long as it doesn’t conflict with something and crash your system. My advice on mods is to have a good saved game before you mod, one that you can always go back to if the mod doesn’t work out. You can also uninstall mods anytime, though that can have some quirky effects…and can lose you a ton of stuff (like, if you put a bunch of stuff in your underground hideout mod and then turn it off, all that stuff in there would disappear).
ETA: Of the mods I’ve installed so far that have worked (the Area 51 mod is the only one that I can’t get to load), I haven’t noticed any undue destabilization of the game so far. The game occasionally locked up or crashed before I added any mods, and it still does…but it doesn’t seem to have gotten worse. I remember when I added the underground hideout mod (near the Air Craft Carrier) in Fallout 3 that it seemed to seriously destabilize the game, but this time it seems a lot more stable.
-XT