This argument is nothing new. I remember back in 2005 GameQuestDirect claimed to have found "lost" warehouse copies of games like Rhapsody, Persona 2, etc. for the PSX and people bought up their stock only to find out they were actually reprints and the company lied to increase demand for the games. And those copies found their way into Gamestop stores, too.
Yep, reprinting is nothing new. They've done this with at least a handful of other games. Off the top of my head, Rez (PS2) and Gitaroo Man (PS2) were a couple prominent titles GQD did this with back in the day. I think they eventually admitted to reprinting them.
I'm sure they're not alone, there's a fair chance publishers themselves are getting into the game, especially given the exorbitant prices new copies of some of these older, classic/under-the-radar/cult-hit games command. Some of the Greatest Hits PSX Final Fantasy games, for instance, have versions with either "Squaresoft" or "Square Enix" printed on the front covers (pre/post-merger print runs).
Speculation, but I think Yakuza (PS2) had at least a couple print runs. My release copy came in the typical old-style Amaray case, while a friend's copy purchased a couple years later came in the new-style flimsier case lacking a memory card slot and with "PlayStation 2" branding above the disc holder.
With Nier, I could see it going either way. $19.99 doesn't seem like it would be worth the effort compared to the prices Xenoblade or Metroid Prime Trilogy are/were selling at, but some of the old GQD reprints were going for about the same price at one point (~$25 IIRC) so who knows. We simply don't know the cost involved, whether or not companies have some sort of licensing deal or are just handling manufacturing or logistics for the publisher, or really anything specific about the situation.
On the other hand, it's certainly possible they found a couple pallets in a less-traveled warehouse somewhere. Stranger things have happened.
All that aside, I gotta go with "who cares?" I am a big proponent of the old argument that games are meant to be played. I don't agree with Gamestop's pricing or their practice of selling these games pre-owned rather than sealed, but if they're getting these games in the hands of gamers cheaper than through eBay, more power to them.
Would I be annoyed if I were sitting on copies of previously rare games with tanking values? Sure, but that's a minority compared to people who are actually interested in playing some of these titles, and anyway that's an inevitable side effect of buying games with the goal of reselling.