Take this with a grain of salt (and I'm also a firefighter, so you know you can't believe half the shit I say anyways, haha), but in my TJ, there was a small subwoofer and amp under there. It was blown, so I removed it. Now there is nothing all the way down to the floor. I plan on enlarging the storage area. But again, I am unsure if the JK is setup the same. I assume you are going to drill the hole to put something in there, so why don't you just remove the storage piece and see what is there. I think it is just a few screws to take them out.
Hopefully someone with a JK can chime in and give you some better info.