Putting in spike pits and rockfall traps at the entrance would make it really annoying to leave the place quickly if they do somehow find us. But that's no reason not to put them in half the fake boltholes. Anything that will make them more time consuming to search is a plus.
You misunderstand what I meant. You described the trap thusly:
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| |x--
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|__|y
x is where we would be hiding. Now, the traps I described would be placed at y, the spikes facing downwards.* If we choose to leave, all we'd have to do is disable the rockfall trap (which should be easy enough, just unhook it or whatever) and then drop down. The spikes are ringed in, facing down. You can drop OUT easily, but climbing up IN is when they become dangerous.
*The rockfall trap would obviously be up on the ledge to the place where we are hiding, to give the rocks some time to pick up some good speed, but the trigger would either be hooked to the spikes, to prevent the baddies from removing them, or be a trip wire or something, strung over the entrance above the spikes. Also, it would be best to place the spikes RIGHT over the surface of the water, preferably almost touching it. Because the baddies natural instinct after coming through the tunnel-of-unknown-length-filled-with-water should be to surface... Into the spikes.