When I wrote up that analysis of the % In Lair column from the Vol. II monster table, I was working on the assumption that this was meant to be a percentile die roll to see if the monster is in the lair when the party enters. That's the way I used that number. I have also heard of people using it to determine if a random wilderness encounter means that the party has discovered a monster lair as opposed to wandering monsters.
But I'm wondering if it is really meant to be a multiplier for stocking monster lairs: when creating a bandit camp, 15% of the total number of bandits will be in the camp proper, while the rest will be on raids, at guard posts, or about to arrive back.