I have already mentioned some of this on the xonotic IRC channel... I'll also post a "short" summary here again. I'm no lawyer or law expert, but I do have some law courses as part of my studies, so I have a brief overview (mostly about the german law system, though).
Xonotic surely does not violate any licenses, this is crystal clear.
I *think* Lee and Havoc both don't violate any licenses or copyright. They might have "licensed" the Nexuiz name, which, as far as I understood the discussion, was never actually trademarked. So they were licensing something to IllFonic which didn't even belong to them. Well, that's sad for IllFonic if they are dumb enough to pay them money for using a free name, but that's of no concern for the legal matter of Xonotic and the devs.
IllFonic MIGHT be violating licenses. For them to violate anything, they first need to release a product to the market, though. Unless anything is released, you can't put forward any claims. Obvious.
Now the situation gets a bit complicated. If, from looking at the product (the finished game) people recognize their work in the game, they may pursue legal action (should be especially easy for the data part, if you see models, levels, etc from the original game which are GPLed, you've got your hook). For other things it might be more complicated. You can't directly see GPLed work in the engine by playing the game. Things might have been rewritten or left out or are simply too subtle to recognize.
If the license holders of the GPLed code in the engine want to actually pursue legal action (legal action is, of course, not necessarily required. If the involved parties think everything is fine the way it is, then the whole discussion is senseless and development should be pushed forward, instead
), then IllFonic maybe could be forced to release the sourcecode, to make it possible to inspect it, in the first place. Even if the "opensourcing" would be limited to a small circle of people only, which then can examine the code for GPLed work. Something similar happened to Linksys and their WRTG router firmware. They used linux and original iptables code, which is GPL and were forced to release the software. Based on that code, all the OpenWRT, ddWRT, etc, router firmwares were created.
As I said, I'm no law expert. If it's the wish of the license holders to pursue legal action and maybe force IllFonic to opensource the code, so benefits can be brought back to Xonotic and others again, it would be wise to contact professional help. The Free Software Foundation might be a good start. They have lawyers and afaik they help open source projects for free, if it's all about GPL and the like. You might contact them, discuss the matter and see what can be achieved by legal action (opensourcing of IllFonics code, maybe financial compensations, whatever), you'll see how long it takes, what resources the process will eat and what sideeffects may occur.
If you are undecided about what to do, talking to some professionals surely won't hurt, as that doesn't imply legal action already.
Hopefully I was able to shed some light on the legal side, unless all of that was known already
Anyway, I hope Xonotic 1.0 will be a blasting release. Looking forward to it