You should talk to your JAMF account rep about that. Its a bit unclear. Windows computers show up as unmanaged devices since Casper can't actually manage them, just collect inventory. Whether they eat up actual licenses though - I'm not sure, but I think the answer may be yes.
We have some unmanaged mobile devices in our JSS (basically just inventory record, we don't manage them in any way since they are testing devices for our Development team) and we don't pay for those licenses. I get the impression that your seat count is for managed licenses only. Though, again, your account manager will have the correct answer to this question.