There are some very slim subwoofers available nowadays, mostly meant for fitting behind the seat of a ute where there isn't a lot of depth to fit a normal sub.
We did a lot of measurement and sizing of various subs when putting the doof-doof system in our fun car, a '57 Morris Minor (yes, really...), and because of the restricted space in one of those, we came across quite a few ingenious subs which don't take up a lot of space. (We ended up with two ten inch subs in the Morris).
For our VX Lumina, I have been considering a ute-type slim sub presicely because of your same concern, namely boot space, as we do a lot of travelling and need the space.
We may end up fitting a pair of slim ones, either side of the fold-down opening so we can have the best of both worlds, namely boot space, subwoofers, and also retaining the rear seat opening for boot access and longer items.