And kill an enemy faction does it effect your reputation even when you're "disguised" ?

seems to be hit an miss.

I dressed up as legion and killed some rangers to get the veteran armor and lost no karma or rep. (let them attack you first!)

I tried it again a while later at a different camp and suddenly was hated by the NCR, though this may be due to killing a named NCR toon, I haven't bothered to test it out more yet.

just save your game, go kill, see what happens, you can reload your save it you aren't happy with the results.

Rule of Rep changes 101: they must attack you first or you get a Rep hit.