Andy:
I think you've got the order backwards. If you're going to drop in bunkers at random, I think you should do that BEFORE the architect locates the greens, so he's got some more to work with. If you really do the bunkers at random after the holes are set, 60-70% of the bunkers are going to be in spots that see very little action ... you're going to need a lot of balloons if you want more than a handful of interesting holes.
The thing about bunkers on real links courses is that a lot of the bunkers that appear to be random, probably aren't. They're in areas that were getting worn out in the early days from high traffic and divots. If they were in play back then, they're in play for some class of players today.