See https://en.m.wikipedia.org/wiki/Usage_share_of_operating_sys...

(Scroll down to servers)

Incidentally this is public facing Internet servers. The % -inside- enterprises us much much higher.

Tools like Active Directory allow you to scale enterprise operations, which is important for companies that have hundreds-of-thousands of desktops etc.

In any event your estimate of 99.9% is unlikely. AWS offers Windows based EC2 instances, and one presumes they're not doing that for 0.01% of the market. Azure will likely have an even higher %.

From the data though, not just guessing, I'd say it's about 20% overall.