I think the perceived problem is how accepted it is among the games, even the "serious" ones, more than the lack of any real attempt to make it "realistic". It's like not seeing your feet in an FPS - unreal, yet universally accepted. Some people are still bothered by it, of course, while other couldn't care less. It doesn't necessarily mean any group is particularly more in the right.
The difference between these examples is, while it would be exceedingly hard to offer any kind of justification for the FPS Ghost Syndrome, RPG floating invisible scabbards have it way easier. Just have the weapon bathe briefly in golden light any time it is put on/off the hero's back. Voilà. The world is consistent, floating makes sense, badass points are scored. The game is arguably more awesome as a result. Not doing this can only be attributed to being lazy or dismissive.
The only problem is can see with it, it changes the world. A realm that allows for such an everpresent, utilitarian arcane power can no longer be a perfect Tolkien fantasy. Some people might have a problem with that. Ultimately, from the creator standpoint, it comes down to the difference between creating one's own world or maintaining a flawed masquerade. You can either tell people to imagine the scabbards being there, floaty and possibly invisible, or decide to just fuck Tolkien and actually try to think up something yourself.
Which, of course, brings me back again to the conclusion that studios are lazy. There's little to no excuse for that.