[Austin]

Todd from TK Instruments puts wood veneer covers on his pickups. Check out this guitar for example:

wood covers

[NiCkMiLnE]

Originally Posted by Drew

Heh. Mount from behind.

[sepherus]

Totally possible, and awesome concept! make sure the fret board pretty much comes even with the body, route for pickups, add veneer overtop. The hard part would be making sure they are aligned properly, although I suppose you could set all that up pre topping it. If doing it with an actual cap, just route that out a bit from the underside. the wood is magnetically inert, so it won't effect the sound much if at all. A removable solid wooden pickguard is another option that would look spiffy that would allow you to change stuff around.

As for pickups, I would use some thing fairly hot a least and 1 meg pots if it is going to have to be backed down a ways. There is always the option of a preamp booster in there too like an Afterburner, PA2, or similar if you really need it. I want to do this with the 6er im building now....

[Apophis]

^^

[Demeyes]

I've been thinking about fitting a piezo transducer in the trem route of one of my guitars and then wiring it into the electronics if it sounds anyway usable. I've heard people do similar things before. I don't use that trem much so I'd put some foam under the springs to quiet them down a bit.
As guitars with hidden pickups, I've always like the look of the variax. I had no idea what was going on when I saw that first.