This is exactly the reason why I said I didn't care if I get lair enemies back or not, but felt it important to mention it is not a micro-mechanic but a mechanic that causes (a tiny bit) of dungeon construction complexity. I'm perfectly happy with alternatives.
And yes, dungeon keeper has quite a few mechanics that are not obvious to players. Some of them are mentioned in one of the millions of messages that show up, but that hardly helps of course. Such mechanics are always nice if they can be discovered by the player, and angry researchers and lair-enemies to some extend are. If fights break out they can follow the creatures and easily find out why. First they learn they should have separate lairs and should not send in bad researchers along with their warlocks, and after that if you notice you still have some but fewer issues you can observe your rooms to see what happens and you'll find out that traffic through the room causes those issues. The player can now think for himself to decide that another dungeon layout will help with these issues, or using different creatures, and he does not need to get the solution spoiled.
Having alternatives for traffic is difficult, as you want to make it obvious there is a problem and how to quantify it. You don't want something like the DK room efficiency, where I believe over 90% of players have no idea what their room effectiveness is, why it is not 100%, and that a 50% efficient room really slows down training/work/storage by 50%. When you look at the tiny room flag, those 3 little bars communicate very little unless you really know what to look for. This went so far as that even the WftO developers did not now it existed or that why such a system is crucial to have and they released their game in a state where the optimal dungeon had no walls at all and all rooms build right up against each other.
So if traffic has a detrimental effect, think of a way for the player to discover this. Say what you want, but in DK the creatures starting fights or shooting at each other is at least a very clear tell that something's up.