Hyper-threading enables a server to split a single physical core into two logical processors. Again, there is no magic here; this does not double your performance. There is no explicit supportability statement around hyper-threading for Lync, but general guidance is that hyper-threading is not equivalent to dedicated cores.
The host server operating systems/virtualization platform is not going to consume many CPU cycles, so for planning purposes in most cases it is acceptable to ignore trying to dedicate a core to the host. If cores for the host were included, everyone would wind up with an odd number of CPU cores.