Customizing cannot be undone, thus you should only customize weapons you intend to use for longer periods. It doesn't
completely lose it's value, as merchants still will buy it for scrap iron price. Or you can try salvaging the weapon mods off it with expert salvage.
Customized weapon does 20% more damage, so that's the point in it.
edit: hurr, fine, 20%! I can't remember everything, especially at work :P