Hm, interesting. I own an NES Classic myself and did successfully load my own up with hundreds of extra games using Hakchi2, but some of the hacked/patched games either did not transfer over at all or transferred over in a screwed-up fashion. For example, the FF7 NES game (english patch applied) did not transfer over, but The Legend of Link did, although it has some severe tiling errors when displaying the intro (which, if I understand correctly, means that I am going to also see some severe tiling errors in the later dungeons, which sucks). Most discussion I've seen on the NES Classic seems to only cover how to load it up with extra games in general; niche examples like mine don't come up often so I'm unsure how/if it can be corrected at all.
I had considered adding additional emulators, but thematically (to me) it felt "wrong". To each their own. But this is also why I really want to secure myself an SNES Classic (and depending on reviews of the Genesis Mini's audio/video quality, one of those eventually): so I can load it up with its own respective library and hope that all of the games with special chips emulate properly.