Critically this only works for the bioengineered microbes that produce marker molecules that the hyperspectral cameras can identify. This doesn't work for random microbes out and about.

Here's a company which produces biomarkers (which it can disperse as aerosols or via other means) which it can then detect in air or other samples: https://www.safetraces.com/

(I have no commercial connection with them.)

Then we infect every microbe with that biomarker and make hell real for germophobics?

Or a less dumb application: lab leak monitoring

There are people pushing for the use of microbes in farm land instead of chemical fertilizers. These markers would be useful to see what plots are treated or not.