I understand your concern and agree with the basis of the concern. You'll find many discussions in the forums about the topic of additional licenses for a subscription.
It is my understanding that this is a Billing system issue and that there should eventually be a solution for it. In fact, I am surprised that we're still in the same situation as it was mentioned during the 2.0 beta that something was coming to address this. No time frame was given, but... Right now, I have to assume that the solution isn't too far off as OneCare for Server, coming with the next version of SBS should be available later this year - 2nd half of '08, according to the press release. I am sure that deploying OneCare to clients from the SBS server isn't going to require multiple LiveIDs to exceed 3 copies!
As for your current situation, as I noted, there is no technical reason for limiting the number of PCs. There is a hard limit of activations that can take place, though. You'd have to reinstall all of your PCs a few times in order to hit it. In the event that they do decide to restrict your subscription to 3 actively running copies, you can bite the bullet at that time and reinstall. My personal advice (I don't work for Microsoft) would be to shelve the second licensed copy for now and consider that key used - don't use it for another subscription as long as you are running more than 3 PCs on your first one. ;-)
-steve
