We've spent several years trying to get pregnant, and had to resort to several rounds of IVF before success. Yes, minimally researched terahertz body scanners that are mandatory for travel keep me up.
You have my sympathy. That's a really difficult thing for any couple to go through. Still, in that case, you're probably trying to control a lot of other variables that already rule out air travel, no? For routine pregnancy there is no risk from EM identified in the literature that I know of.