A buddy of mine unfortunately had all the stuff stolen from his boat, but the only the d**heads didn't steal was his tower speaks - he had some special screws made with a unique key head to them. So basically if you wanted the speaks without the allen-wrench style key you'd either have to hack through the tower or the speakers themselves.
Just another option if you don't want the alarm (which is not always effective).
If you know the length and thread you need McMaster.com has some good security bolts like this: