Yes it is. I found this link when I googled 'Windows for Submarines' when I read about it in Eric Schlosser's New Yorker essay "World War Three, by Mistake" which was featured earlier on HN.
Do not assume technology has been rolled out just because an article was a while ago. The military deals with just upgrading a version number of software very seriously and it takes years to happen. I can personally attest to Windows being installed on computers emulating a submarine environment. (it was probably XP)
I don't know why the age of the article is reducing your fear. If anything they probably do more and more this.
And the OS is out of service (thank god :)) but the submarines running it aren't (oops)
I guess that they can think about upgrading from XP right now.