Just finishing up my trip and happy to report that I had some success with a little special treatment while pregnant. At SFO (Terminal 1 - Delta), I opted out of the millimeter wave, and had to undergo the full body patdown. On my return at JFK (JetBlue Terminal 5), I was initially directed to a millimeter wave, but when I told the TSA agent I was pregnant, he let me go through the regular metal detector instead, with no patdown needed. I'll take a 50% success rate these days! So, long story short - YMMV.

I don't think that there would be any evidence anywhere that can demonstrate their safety. They have not been around long enough to look at it prospectively to assess harm, nor have they been tested (to my knowledge) on pregnant animals to infer risk to humans.

The likelihood is that they are safe. (not forget we are all being exposed to low level ionizing radiation at cruising altitudes which if you fly a lot may expose you to increased risk of cancer death, albeit very small contributor)

That being said though, as long as you're comfortable with a physical pat-down and the delay this may cause, I do believe that it should be the right to decline any scan while pregnant.

When my wife was pregnant, never was able to get the WTMD when opting out.

That said, the other thing we tried to keep in mind was to keep her from staying in close proximity to the luggage x-ray tunnel. The luggage x-ray has significantly more power than the AIT, and some level of leakage is likely. (So when opting out, and asked to stand next to tunnel, she would ask to stand at a greater distance - and always was accommodated).