I would consider it unlikely that airborne germs form a significant input to our microbiomes.

For example, the gut microbiome is in flux for about the first 3 years of life, and thereafter it's mostly only the relative abundances of different microbes that shift in response to diet, you need something like antibiotics or severe diarrhea to actually induce permanent changes (usually for the worse).

Compared to that, there really aren't many microbes in the air. For children, it could very possibly be bad, but even then I'd expect most of their microbial input to come from their parents, food, and surfaces. Which are already grossly deficient compared to old-school rural settings, but I'm not sure if germicidal UV would make it worse.