Sure third party games aren't the "selling point" of Nintendo consoles, but they're still really important. And ever since the N64, when people hopped over to Playstation because they embraced new technologies, it's been hurting them. A lot of people will then bring up that the Wii was a major success, but that's because they came out with the right gimmick at the right time and after it's novelty wore off, the Wii was pretty much, "oh yeah, that's a thing"
Downgrading stuff for weaker hardware is something Devs already do regularly, but like you said, it's not the easiest task. It might not be bad now, but if/when devs move to the PS4 Pro and Scorpio as their lead platforms it'll just get harder and harder and eventually downgrading for the Switch could become not worth the effort.
As for the multiple control scheme thing, they may not make it mandatory, but we don't know yet, and devs who haven't worked on Switch games yet are probably concerned about that. If Nintendo is cool and doesn't mandate that games have to work for this and that control scheme, then that's a plus. If they do demand it, it's going to be tough for games that require something that a separated Joy-con doesn't have, right stick and d-pad being the biggest issues