If you're very sure that none of your software applications relies on .Net 3.5 then you can safely uninstall it. If you're not sure, leave it be.
Programs can occasionally freeze for a second or two for a virtually unlimited number of reasons. You need to be very sure that .Net 3.5 is causing that before you think of uninstalling it.
The issue here is that many well-meaning users make changes to their computers that they don't really understand, and when their computer seems to keep on running they figure no harm done. But frequently harm has been done, only it doesn't show up until later, like the next time Windows tries to install an update and 'suddenly' their computer is crashing.