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Laymens guess what problems it could introduce:

Vacuum does not dissipate heat well (extra engineering in that department)

Vacuum is never 100% vacuum. If you have some dust in the air, it will mostly flow to the direction of the airflow, but in vacuum dust particles will do random walk thing and settle on surfaces.

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Plus the fact that then you need the everything to be structurally strong to be able to support 1atm of pressure differential, keep the vacuum sealed, and keep material degassing under control, so you end up with some heavy duty, expensive stuff. Pretty sure a lot of steps in the chip fab are done under very very high vaccums tho!

In general it's easier to control the air you're blowing into a room than what you're extracting, so I'd expect it would be more economical to keep the fabrication rooms under high pressure than low pressure. Also, in case of a leak, air and contaminants will flow out of the room instead of into it.

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