Once you've been fingerprinted once, how many times you are fingerprinted after that is, in the end, meaningless. Additional prints are merely a confirmation of your identity. They do compare fingerprints between agencies, as Layout said. When I was fingerprinted for HAZMAT, they compared those to the FAST prints to make sure I was who I said I was. When I renewed my HAZMAT they took new prints and compared them to the previous ones. Unless you're trying to hide your identity, or have stolen someone else's, or plan on committing an evil crime (as opposed to a good, honest, upright and moral crime, I guess) there's really no real reason to fear being fingerprinted.
Do you miss out on a lot of freight if you don't have HAZMAT? Probably not, but it depends on the carrier. Some carriers require you to have it because they haul a lot of HAZMAT loads. If you sign on with them and don't have HAZMAT, and if a lot or most of their loads are HAZMAT, then you're gonna miss out on a lot of freight. Other carriers haul some, but not a lot. In any case, generally speaking, the cost of adding the HAZMAT endorsement to your CDL is really small considering the fact that a single HAZMAT load that you would have otherwise missed will pay for the endorsement. At other times you may be hauling a HAZMAT load where if you didn't have the endorsement you'd simply be hauling another load, instead. If you're with a carrier that pays the same for HAZMAT as a regular load, then there's no real reason to obtain the endorsement, unless HAZMAT is the primary freight for that carrier.