The other cost would potentially be porting a bunch of specialized apps over to Linux. JMPS is one off the top of my head. No idea what stuff like that is written in or how cross-platform it is, but dev work costs big bucks.NMCI is an enterprise solution for every Navy employee. By using a widely proliferated OS we ensure max compatibility with others and ability to use many COTS apps while avoiding a huge.training overhead because most are familiar with the windows OS. USN doesn't want or need to sustain an in house Unix system. With a few exceptions most employees need a box that can do the email and some internetting. There are other solutions available for people who need more horsepower.
@antonkr I see you're in undergrad CS at the moment. I don't know how much Windows/MS hate gets thrown around by the faculty, and yes, there are a lot of tech companies out there that have chosen to be Linux shops for various reasons. But Active Directory and Windows sysadmin type stuff is still absolutely a thing that can make one a career in the private sector for just the reasons @Pags described. I personally work in a shop where my devs will throw VS Code or IntelliJ (language dependent) onto a Windows desktop, pull down a local copy of a Git repo, and get to work. It's not unheard of even in tech. People know Windows. People know Office. Linux distros are definitely getting better, but every time I play with Linux, it seems there's always some amount of higher nerdery and Bash commands that seem to be required to un-futz things and get it working just right. It has its uses, but to create a regular old desktop, it's always seemed to be about 110 percent of the work to get 85 percent of the functionality of Windows. In tech, it's important to pick the right tool for the job . . .