I get clear fluid filled bumps on the inside of my cheeks. They don't hurt but are annoying, I scratch to pop them. What are they, what causes them?

Mucoceles? There is no way to know for sure without actually clinically examining you. However, they may be mucoceles which are little fluid filled sacs from blocked ducts on the many minor salivary glands in your mouth. If chronic, have your local dentist examine you just to be sure.
Mucocoel. Sounds like small saliva filled bubbles. They are self limiting. Have them checked to confirm.
Sliavary duct issues. If somehow you block a salivary gland duct it will fill up like a small cyst with clear fluid and if you pop it will go away. But since the duct is still oblitereated it will periodically come back.