Either way, it's not likely Windows is all that significant in terms of MySQL usage or you'd be seeing more activity and movement on that front. And Windows developers aren't really all that open source savvy yet either ...
Licenses can cost quite a bit when you have lots of systems. A former employer of mine saved several hundred thousand dollars by moving from MS SQL Server to MySQL and PostgreSQL.
You're probably right that there's no technical reason to use MySQL on Windows, so the only reasons left are management reasons ("our code monkeys can install whatever they like as long as it's on our trusted Windows (tm) machines"). This explains why the technical support for MySQL on Windows sucks, while the management support is prominent...
There's also a trend, at least in performance centric circles, to start building from source with patches or using third-party binaries, like those provided by percona, and other stuff not provided for on the mysql website.
Downloads from any one website are ultimately not indicative of the actual usage of the software, especially when it comes to freely repackagable open-source.
From a short-term management perspective it seems better to have just the promise of support than to have nothing at all, but in the long term you're sending a signal that MySQL on Windows isn't to be taken seriously, and that you don't want people who are committed to Windows as customers. That's as fine a business decision as any, but then it's cheaper to cut out Windows development altogether than to go about it halfheartedly.