They generally have a light-up sign at the toll booth that shows if the transponder battery is getting weak. I think all the EZPass transponders do have a battery, though not all RFID systems (of which it is one application) require a battery; some are powered by the radio signal itself from the reader.
If the battery is dead or the transponder otherwise fails to read for some reason, it bills your account based on the license plate reader. I think if you go through too many toll booths with a nonfunctional transponder there may be a penalty or fee or something.
For the most part, EZPass just works and works pretty well and the strange odd edge cases really aren't worth worrying about. Verifying one's statement against reality is, of course, not a bad practice, just like checking one's credit card statement.