SM and USUM were released after the New Nintendo 3DS so I think it's likely. I mean it's not like Nintendo is super big on making things equal; Japan getting exclusive events (including legendaries that other regions haven't seen for years previously) and systems, so it's not like they would refrain just because some people don't have a NN3DS. In fact, wouldn't it make them want to do it more because then people would have to buy the system?
In all honesty I'm not sure what content they would put in an amiibo. Pokemon I guess like Mew snd Celebi but that feels very one-time, and amiibos generally have more than one usage.
However, I definitely feel like it will come eventually, if not in USUM, definitely the next game. Nintendo is pushing more towards including purhases for more content (overpriced DLC just for a single class in Fire Emblem Echoes, needing dozens of amiibo for all content in Breath of the Wild as well as exclusive stories, pay to play DLC and content in nearly every main Nintendo series. It's coming eventually.
Not too worried though, Pokemon is extremely hackable and exploitable... things never actually stay exclusive.