Maybe I've pointed this out elsewhere -- actually, I think I mentioned it in my RAM offsets post -- but the limitations on enemy count is self-imposed. You can change it if you want. There are basically four types of enemy spawners I've encountered so far:

1. Instance slots 1 through 9 (0 is reserved for Trevor) are checked if currently occupied by the enemy to be spawned. A counter increases with each enemy spotted. If the count is less then the specified number (and 3 shalt be that number), slots 1 through 9 are checked if empty once again and the first empty slot is used to spawn the enemy.
2. Instance slots 1 through 3 are checked if empty and the first empty slot is used to spawn the enemy.
3. Instance slots 4 through 6 are checked if empty and the first empty slot is used to spawn the enemy.
4. Instance slots 7 through 9 are checked if empty and the first empty slot is used to spawn the enemy.

As you can see, in spawner type 1, altering the value checked will allow you to spawn more than 3 of any one enemy. In spawner type 2, shifting the higher value will allow you to spawn more than 3, but if you do so you should also change spawner type 3 since often they co-exist. If you change type 2 to search slots 1 through 4, change type 3 to search slots 5 through 7 or 8.

Bear in mind changing the upper bounds beyond 9 will affect other instances as well. Projectiles are almost exclusively spawned in slots 9 through 12 (four total). I think luminaries are spawned in the rest of the slots. Active terrain (e.g., platforms, crushers, trap doors) occupy spawn slots as well.

You can change the spawner types by altering the values as specified by the offsets denoted in the object info boxes in reVamp. A bat showing 0D will use the spawner code specified offset from RAM address 0Ax8523,1A (shifted left since each address occupies a WORD).