It's worth considering that the name was in Japanese in the raws so it's plausible that the (unaware) new owners didn't understand it. Regardless it was likely that they would've tried to get it off, but it's permanent marker most likely.
The missing moulds were actually tracked down, read about it
here.
About the AE86 moulds, apparently (who knows if this anecdote is equally real) the pictures and videos of the "reproduction shell" isn't really a "reproduction shell", but a real body that just happened to be in that state for some other purpose. Comment
here.