well i have only seen people talk about replacing the factory subs, but i haven't ever heard any so i dont know if that is a good ideal or not. it seems that there is only one real option for 6x9 woofers, i think they are the CDC's
as far as cam's box, thats weird, ive never seen a sub like that before and that is a super small box, if you could find something like that it would be pretty cool.
my cousin has a 2000 LS, and the early first gens had a slightly different sub setup, instead of having the 6x9's and the amp mounted right to the rear deck lid, there was this big molded plastic enclosure that held the speakers and had the amp mounted to the bottom, it took up just a little more space then the newer way, but the whole module bolted right up to the bottom of the rear deck.
now what i did for his car was i took out the subs and amp, then i covered up one of the sub holes with a piece of MDF, and then made a mounting ring for an 8" L7 and fiberglassed the mounting ring right to the plastic enclosure. so that the sub lined up perfectly with the speaker hole, after enough looking he found an amp that barely fit in the stock location(it was only around 350-400 watts which is a little low), we had to take a blowtorch to heat up and re form a couple of spots to make room(not fun) and the results were pretty good, since he was using the factory radio, we soldered a RCA connector onto the factory signal wires right at the factory plug, and he had to find a low voltage relay online that could be triggered by the factory 5v turn on, then we just had to run a new power and ground wire from the battery. it sounded much better than the stock subs and went a good bit lower, the biggest difference was that it didnt fade out nearly as much on the top end as the factory's do, my only down side was that it didn't go quite as low as i would have liked it too (a: i'm am used to ultra lows from my 15"s, and B: it only is an 8" sub, so you cant really expect super deep bass with out big drivers and a lot of power)
now i dont know if the holes are still in the 2nd gen rear deck and if that could be an option for you (im sure that holes could be drilled) but i'm sure that you could make a custom box that was very small that could be suspended from the bottom of the rear deck that could do the same and either hold a good 8" or one of those slim 10" subs.
other ideals i've had would be to remove the factory jack and tire iron and relocate them, and sit the spair tire upside down and fiberglass a small sealed box for an 8" that could fit into the spare tire, this would take up no room at all, but might make the floor of the trunk rattle a bit, and it wouldn't be as loud as one hanging from the rear deck (at least i think any way, since the sound could travel right through the factory subs opening) this is a trick that ive seen in a lot of acura's with the Bose system, a friend and i did this in his nissan a few years ago, but it wasn't nearly loud enough for him so after a couple of months he just put in a regular set of 12"s and gave up on the trunk space.
it also shouldn't be too hard to build a small box like cam's was as long as the sub was pretty small and didnt need much air space in the bunch box.
