The reason opt-outs have dropped to almost zero is because the TSA has exempted from the scanners the groups that are most likely to complain: airline personnel and frequent fliers. Those people can get pre-check and therefore don't need to opt out anymore.

With regard to safety, it depends what you mean by safe. Are you going to drop dead if you walk through a scanner? Of course not. But is there a long term risk? Who knows. It's like asking if junk food is safe. Millions of people eat it and get by just fine. But that doesn't mean it's "safe". There have been cases when chemicals generally deemed safe were found to be hazardous decades after entering use.

I still opt out whenever I am "randomly" pulled out of the pre-check line and sent through normal security. I don't see too many people doing it anymore, but the staff can handle it without any problem.