First, I think it's much more likely the NSA has already
compromised one or more existing botnets, as opposed to
screwing up Windows. That's Microsoft's job!

Try this on for size. Everybody's heard about the
secret room(s) at AT&T et. al. run by the NSA and supposedly
designed to slurp up all the internet packets, telco phone
meta-data, etc. Perhaps they are covertly working with
the backbone operators to provide peering points where
they can *inject* massive amounts of traffic generated
by their own custom dedicated servers. It's more reliable
if you have your own botnet.