All have the same meaning. Yup and yep are more informal than yes, so definitely use yes in more business like settings or conversations. Yup and yep are more slang/friendly. I rarely see yep used other than people who are very happy.

This is casual speech - yup and yep have the same "register". If you're ever in doubt about which expression to use, just use "yes". You can't go wrong with standard English.

Nope, no difference.