If you opt to work for Mr. House or you decide to take over New Vegas for yourself, you will get crappy Securitrons supporting you in the last battle and I think it might affect how good things turn out in the ending.
Not necesarilly.
I upgraded his securitrons before killing him, and i got the super duper securitrons.
Oddly enough, after having progressed somewhat far into his quest line, entering his secret room didn't make the securitrons hostile.