Will the amount of saves I have made make my game more buggy? I play around 2-3 hours a day and since 1.4 I've encountered ALOT more bugs. I've got around 350 saves over 160 hours. Waypoint markers are jumping and I've got misc quests that can't be completed as I can't get to where I want to go.

A high number of saves does not create bugs. I have something like 2500 saves.

Yeah something I learned long ago with Bethesda games is to save, save and save again. I may be wrong but I don't think the new patch will effect already existing bugs, it will sort bugs out in new games, but as I say I'm probably wrong.