I'm mounting my system in the spaces between the rear wheel arches (PC on one side and amps on the other) as I cant loose the spare, I drive to Poland quite often lol. Also use the boot so much that anything on the floor of it would get scratched up/broken etc.
The two silent running fans will be easily enough really to cool the entire system (2.5 C2D CPU etc) so the noise won't exceed the fans maximum 22db ratings unless the boot exceeds silly temps which is unlikely (being in the UK!). Even in 34c weather I've got to say my boot remained fairly cool.
If you think about it, laptops these days are nearly silent running (at least my asus is) and they've got 3+ ghz processors struggling with vista and an over engineered graphics card too... So efficient cooling solutions are about
Watercooling rigs always look good which I guess was one of the major considerations when you decided to go down that route.
I'm enclosing mine behind perspex like you have (although thinking of using UV reactive perspex) and will have several displays mounted in the PCs enclosure displaying various stats... Most of which will be just for effect lol.
The perspex will be laser etched too with some fancy design on it, looks great with UV perspex and a blacklight or just normal perspex and some EL tape on the edges.