I don't doubt that health harms are minimal if any, but every time I go through these I get a very weird sensation in my torso which I'm just not fond of, so I've started opting out since December.
I personally don't mind the patdown at all, and the TSA personnel have all been professional each time I've requested to opt out. I do wonder what would happen if a significant minority started opting out, since that would most likely clog the system pretty badly.
I've opted out every time I've ever ended up in a scanner line, but the millimeter wave stuff is absolutely significantly more safe than the backscatter, specifically because it doesn't use ionizing radiation.
Of course, it's also easily defeated[1][2] by anyone that knows what they're doing, so it's not like it's keeping us particularly safe.
From TFA: "TSA has contracted with L-3, Smiths Group Plc (SMIN) and American Science & Engineering Inc. (ASEI) for new body-image scanners, all of which must have privacy software. L-3 and Smiths used millimeter-wave technology. American Science uses backscatter."
The L-3 Communications scanners are millimeter wave. They do not share the possible dangers of the backscatter machines.