Here's my take (FWIW):
I had a MIM Fender jazz upon which I replaced the neck with an Allparts neck. I bought a Fender decal and affixed it, but was just never really happy with the bass in general, so I parted the bass out (sold the neck for dirt cheap to a fellow TBer whom I told that it was NOT a Fender neck and, besides, the decal work looked like crap).
A few years ago, I bought the best Stingray ripoff I've ever seen off ebay for $175.00 (it was active, tiger stripe maple body and the headstock was EB copy to a T). The thing was so spot on that I placed it side-by-side with my real Stringray and was amazed at the detail, all the way down to the fretboard dots.
Anyway, I proceeded to sand off the existing headstock logo and replace it with a vintage MM Stingray logo (I know, I know :scowl: ) after having done all kinds of other mods to it (S-D pickup and pre, Hipshot tuners, etc.). I have always felt "icky" about this and, as such, I've never played a gig with it (I've only practiced with my band with it and I told them it was a fake the first time I pulled it out of the box) and recorded with it (it is an AMAZING recording bass!). Eventually, I'm going to sand off that logo and leave it blank so I can actually play the thing live!
So where does that leave me? Do whatever you want - who am I to judge what you do? - but I just don't feel right about having a counterfeit decal on a copy, personally, and I'll never do it again. It just doesn't feel right.