If the silicon wafers from which the processors are made are so sensitive that workers wear special suits how is delidding a processor possible?
Wafers are extremely sensitive during manufacture, because if any dust or dirt particle settles on it between any process steps, then the following process steps will fail on the contaminated spot.

Once manufacture is finished, and the chip receives its last layer, dust will no longer bother it.

I would venture a guess that desktop CPUs which have thermal spreading lids on them will receive a proper surface treatment for application of the chosen thermal paste.