For a legitimate "rare" console - I imagine mods would lessen the value. However, it would have to be rare. For just basic older consoles, I am 100% positive that my A/V modded Colecovision increases it's value. I'd say the same for other modded consoles that add video enhancements or quality of life features. I already own a Vectrex, but were I to buy another one - I'd pay extra for one that had the mod to eliminate the buzzing noise.

With that said: I'd have ZERO interest in a Vectrex that had the buzzing mod, and was painted purple, with modified LED lights built into the sides. It simply depends on the mod.