Replacement artwork only devalues a game if it is lower quality or different type than the original artwork. Note that there WERE one original run of sticker equipped Ms. Pacs, so sticker sideart is FINE for them.
Upgrading a classic to a switching power supply increases the value, especially if the upgrade doesn't modify the original harness.
Pac-Man, Ms. Pac-Man, and Galaga machines wired JAMMA with JAMMA bootleg PBCs are worth about the same as all original machines.
Replacing the t-molding with correct molding is fine. Replacing it with incorrect molding depends on the machine. You can't get Sega "double teal stripe" t-molding anywhere, so it has to be replaced with other types if damaged.
As for reproduction cabinets. depends on the quality of the work. A high quality repro can actually be worth much more than an original due to condition.
"Wrong cabinet" restorations are worth less than original cabinet restorations. You often see this with Midway games, as there were 3 or 4 different variations on the same cabinet. The shapes and materials were slightly different, but the parts all interchanged. You also see this quite a bit with Nintendo cabinets.
I have also seen quite a few "wrong cabinet" restorations of Williams' games as well. I once saw a Defender in a Stargate cabinet with FULL repro artwork, sideart and all.
But, I wouldn't be worrying too much about restoration value right now. This is the year that values tank. This is not the year to do restorations, it is the year to buy up all the restorations OTHER people did over the last few years.