I'm at number 912 now, I remember I had well, well over 1000 on Oblivion. I've been playing TES since Daggerfall came out, and I've learned you can never have too many saves!
I also had over 1000 saves on Oblivion

and had no problems, however I am worried if it can effect performance for Skyrim
Can't possibly have an affect. I maxed out the # of saves in oblivion and never had an issue and it was modded beyond recognition. I have 200 or so @ 30 hours and am having no issues.
I don't think you have to worry at all, no reason to really. could always go into the saves folder and delete some earlier saves.
I'm always afraid to delete my recent saves accidentally, so I think I won't do that if I have no problems