Have been running 6.6 for a little while now with no issues at all related to it being in Hyper-V

Generation 1 VM under Legacy boot

Found this post whilst trying to migrate our own FMC to Hyper-V.  Hopefully it'll help somebody else out as we've just managed to migrate the FMC from a standalone ESXi server into our Hyper-V environment.  I doubt this method is officially supported...