Oh and btw... hey 1up long time no type! Hated to just tear into the issue like that but I needed to get done with the technical details first.
Mr. Do, myself and a few others (mostly me though) are currently trying to document what outputs are in mame and then deal with any issues and try to get other games hooked up.
To answer your question... yes, they are just hooked up at random at the whim of whoever chooses to do so.
You've really got five types of games with outputs:
Type #1 was immediately supported upon the creation of the output system. These are games that were already hooked up to keyboard leds before the outputs system was created. Since the keyboard leds are now automatically routed to the output system they work (this is thunderbolt's deal) but of course they are almost always labeled wrong.
Type #2 was also immeditaly supported. These are games that had "blinking" artwork before the output system was created. If a game has artwork then it's artwork states are automatically passed on to the output system as well. These are generally labeled better. Also these are generally the first to get "fixed" in terms of games that currently don't have their outputs working because lots of people use the artwork system and Mr. Do will generally bug a mame dev to hook them up when he gets a new scan of their bezel or what not.
Type #3 are games that have known outputs, but they are "complicated" outputs that require precise knowledge of the pcb and a lot of data-manipulation in-driver to be able to send anything to the output system that's useful. Afterburner and the games that run on it's boards are great examples of this. Aaron Giles was a great fan of afterburner, so he personally hooked up the lamps when he made the output system but that's as far as it's ever gotten, even though the output addresses are generally known for all the games on those boards. Open up the source and see all the crap that had to be done just to get INPUTS in these games and you'll soon understand why. I fear these games may never get hooked up unless a fan of the particular game, who also happens to be a mame dev, gives it a go we are screwed. I tried working on afterburner and others a few months back and failed miserably. Because it's a midway board, terminator 2 also falls into this group. Don't get me wrong, it's not "sega y board" hard, but it's still a little hard.
Type #4 are games that have known outputs but the driver in mame is ANCIENT and the original author, who would be more apt to know the memory address of the outputs are long gone. These games probably won't ever get hooked up either unless someone takes interest. As far as most of the mame devs are concerned these drivers are finished and done with, so they are neglected. Fortunately they aren't that difficult to hook up though, it'd just take a great investment of time.
Type #5 are games newly added to the driver. We are very fortunate that the output system is also used for artwork because thus far nearly every new game added since the output system was created has had it's outputs hooked up so mr. do can do a bezel for it. Since the non-artwork outputs are just as easy to hook up, they get fixed as well. This means at least new drivers aren't going to be a bother.
Anyway.. ramble over. I'm currently making a list of all mame games with outputs, but it isn't ready and I'm also going to have a go at cleaning up the output system in mame. So if you wanna help that'd be great and if you have "hacks" send me the drivers.