Clean water does disappear. Not from universe bit from places you need it most. That there's plenty of it in the air or sea or Saturn rings, is little consolation.
These fabs don’t evaporate the water though, they use it as process water, and then treat it to wastewater standards before discharging to the municipal wastewater system.
Assuming the municipality recycles their wastewater, which they would do in any drought prone region, this water will become clean water again.
I read they either dump it into a local river while monitoring it or back to water treatment plant. Some datacenters have started reusing water but for some reason using it more than once is not appealing. Definitely the biggest problem is it’s not always a closed system and dumping it into a river potentially damages the river and makes the area lose their water. A percentage of the water is also lost via evaporation.
It’s definitely not a closed system unless the water from the waste water treatment plant is pumped back upstream of the source of the municipal water which is not how most of these work.