[pocketstar]

>Has there been a study addressing whether these clean rooms are completely counterproductive to their stated goal?

What is a cleanroom's stated goal? Implying the cleanroom's only purpose is for reducing the risk of forward contamination.

Spacecraft will be manufactured in a cleanroom regardless of effectiveness at stopping microbial forward contamination. Foreign Object Debris, payload and bus contamination during manufacture are the primary concerns. For example, dust or condensate on an optical payload would ruin a Discovery class mission.

The stated goal of a clean room is for quality control, reducing microorganism forward contamination is a secondary.