It depends on how it's handled. I'm not sure how this engine would handle it, but in NWN, using triggers to spawn encounters could bog the game to a crawl. The same for heartbeat scripts, which do a check periodically to spawn encounters, or something else entirely. As someone else that finished BG 2 multiple times, the majority of the random encounters happened as you moved from one map to another. The rest of them were scripted events. I know, since they happened every time I played the game. We're not doing any real map zoning right now, instead doing from inside to outside, or outside to inside, and "You have been waylaid by enemies, and must defend yourself." doesn't make a lot of sense just going through a door.
One way to combat a cleared map, however, is to use an on enter script for the area that can trigger while you're on the loading screen. I used this method for NWN, using a script I got from a friend that used it in his module. It was a really clean system, that could even get the player's level, and spawn mobs accordingly. For MP purposes, it didn't fire if someone else was on the map already.