Will space under sub boxes affect sound?

i have a Grand Cherokee with three amps with four .5 farad caps and two dual 10 sub boxes.

I decided i wanted my seats to be able to be upright and built a two level area in back...

the 2500d, RF301x and JVC 4750 along with two distribution blocks and four .5 farad caps are on the bottom level and 8" above is a 3/4 mdf shelf which hold both sub boxes.

My questions is:
Will the roughly 32" X 8" X 40" amp rack space affect bass?
This space is fairly open and padded on bottom.

Yes, I think that airspace will add a resonance to the overall sound by sympathetic vibration of the platform.  Your best bet, IMO, is to double-layer the platform with a second layer of cementboard on top of the MDF (I'm assuming  you used MDF).  The cementboard is not just nailed or screwed, but is set onto troweled thinset mortar, then screwed down.  That, along with lining the inside of that enclosure with eggcrate-type sound absorber, will virtually eliminate an increase in unwanted frequencies.  Weight is gained, however, and your Jeep may not like it.

-------------
Build the box so that it performs well in the worst case scenario and, in return, it will reward you at all times.