When they bought hotmail, it took them years to migrate off the freebsd boxes that was running it -- they had several failures, and when they finally succeeded, they needed several times as many NT boxes as the original BSD boxes.

I would guess that the supernode software was written by skype long before the acquisition (they were running their own supernodes, despite what the article claims -- although not as many, and most supernodes were users), and microsoft hasn't had the chance or the reason to port them to Windows yet.