I highly, highly doubt that you're right about this. If you happen to be right, you won't be for long. It might be that nobody wants to run Windows, but there is clear motivation, as well as hardware and software technology, to have a full-scale OS on an advanced UAV.
UAVs are very complicated in terms of technology and engineering, but the hardware is simple because it's basically just running control loops on some board.
spoilers: Microsoft has a significant enterprise support organization, which the military is probably already dealing with, and Windows scales farther down than you'd think.
For the only reasons such stupid thing happens: the clueless manager wants the machine to run a modern OS and thinks Windows is the most modern OS out there.
post-downvote edit: I am saying nothing about viruses like Stuxnet, designed as weapons tailored to infect specific systems, for which no OS would be safe, but how brain-dead is it to design critical systems that control airborne weapon systems around an OS that's vulnerable to each and every piece of malware known to man?
I agree I am more familiar with corporate IT disasters where some pointy-haired boss decided Windows was the way to go instead of what would be the optimal choice, but I always expected flight-control software to be built with a great amount of attention to every detail.