This discussion brings up a major point and I think a few flaws in the system as well.
We have several clients with multiple sites. These are things you do with larger clients that have larger budgets. We generally have the array setup like this Dev Site -> Staging Site -> Production site. So 3 sites. The reason being is that the product stays synced with the live site, unless we are pushing a change to the production site. This allows us to have a dev site that we can test things on that will never make it to the staging site. Think about it as failed tests, things that might have seemed like a good idea, but did not pan out for whatever reason.
Its going to be hard to use a restrictive licensing server in an instance like above. I get that a developer might not have licensed his modules to be used in an instance like that, but at the same time I think addons or any store needs to have the licenses more open, they are impossible to work under really. For instance, even with a setup like I have mentioned, I have cloned a site locally to work on while traveling in an airport or else where. Now I am talking about 4 instances of the same module, if my employees want to do the same we could be talking about 8 instances. Are we going to have to have 8 licenses now? I don't think most developers are going to want to pay several thousand dollars in modules just to set up a development site that they can work on locally.
At the same time, maybe some developers know, but most merchants do not know. If you run multi-shop you are supposed to purchase a module license for each shop. This is something that I have always disagreed with. This is going to make the ownership of multi-shop out of reach for a lot of merchants, but at the same time I cannot understand how it is going to be enforced without a lot of changes to the module api either.