Permanent mods devalue a game in current state IMHO unless it's exactly what someone is wanting. Bolt on mods shouldn't have an impact in current or future state as they can easily be removed without damage to the game.

Are you referring to the age of the machine or the actual themes they are choosing to use now?

This is pretty unlikely, unless a mod physically damages a PF, cabinet, backbox, etc. Antiques are valued on their originalness, yes, but lots of things come through the shops with the wrong hardware, for example. If still available, it's swapped out and the item retains its complete value. Repaint or restain/lacquer something, or physically damage it, and then you're talking real devaluing. So overall, if you're applying the same rules as an antique dealer would... then no.