I don't think that running games from SD cards will be a problem at all. I'm gaming a lot on my Legion Go and Steam Deck and put a lot of games on SD card. I didn't encounter any problems with that, even with more demanding games like RDR2, Horizon: Forbidden West or something. Not even the loading times are an issue. So I really don't see why Switch 2 games should be a problem, especially since I don't think the console will be significantly more powerful than the Legion Go. Maybe even a little weaker to get better battery life and a smaller form factor.
Official member of VGC's Nintendo family, approved by the one and only RolStoppable. I feel honored.