Shielding should not negatively affect tone if done correctly. Yes, there can be an issue with capacitance, but unless you put insulated hot leads right on the shielding or cram shielding around pickup coils, it's negligible, and even in those cases, I doubt you'd really hear much. Pickup covers are a different issue due to eddy currents, and that's a whole subject unto itself.
Inside the guitars we started with making sheet copper boxes soldered together. Then we went to silver conductive paint, tried copper paint and didn't like it, and now I mostly use ElectroDag carbon shielding paint.
One of the biggest issues is incorrectly or not grounding the shielding, as ridiculous as that may seem, I've seen it many times. It just makes the problems worse.
Also, you should try to star ground all guitar electric components for lowest hum and buzz pickup.