I would also worry about water if you put the amp down there. Make sure there are no holes in the trunk. AFAIK the spear tire well is used as a drain if the drunk gets full with water.

Trying to make it theft proof is good, but my friend tried to do the same thing. He had a custom box molded to fit his trunk.
Not only was it almost impossible to be removed with it not being bolted down, but every screw was drilled + appoxied. They used a what we guess to have been a jigsaw to remove it.

Honestly I think the best way to thief proof your car is to make it look as stock as possible. If they think your car is just some average joe car, they'll pass it by.