It's your guitar, do what you want. It might slightly alter the value, but as long as you put good quality p/u in it, and you have it professionally done, the value of the pickup should offset(to some degree) whatever loss in value. Do not cut a hole in the side of the guitar for one of those pre-amp, equalizer deals though.
Go fishman like you would find installed from the Martin factory, or mike the guitar. Microphones are cheaper than a good p/u system. JMHO.
I however bought a soundhole p/u that doesn't require cutting holes, so far I don't really like the p/u, but that said, I haven't heard it through an acoustic amp or a PA. Which has to sound better than through my 30watt Crate.
