I seem to recall that games ask for a clock profile and whether the system is docked or not. I suspect that the Erista and Drake will behave differently at the same clock speeds, so a S1 game on S2 may get different clocks than requested anyway. What if they get Just get S2 equivalents to the S1 clocks (a S1 game requesting portable clocks on a S2 sets the S2 to portable clocks that a S2 game would get) and would just plain benefit from the higher clocks in regards to fewer frame-rate hiccups and better resolution in the case of variable resolution.There are PS4 games that got "60fps upgrade patch" for PS5, mostly 1st party games like TLOU2, Ghost of Tsushima and Days Gone. Yet, many PS4 to PS5 upgrades are being handled as "games" rather than patches. Upgrading RE7, RE2R, RE3R and Destiny 2 requires you to download a "full game" .The shop and the console after downloading show them as PS5 games, separated from the PS4 version.
Nintendo wants to entice the current Switch fanbase to jump to the next gen especially with the whole "smooth transition by Nintendo account" thing. And they definitely want to grow these sweet NSO subscribers numbers. So I think it's quite possible to make the upgrades part of NSO subscription while being sold in the eShop separately, much like how they are handling DLCs right now.
Either this or that, I'm sure that 1st party upgrades won't be free lol. But we have to wait and see.
This is a half formed thought with no research, but I don't expect that any games should have problems with running at higher clock speeds than normal.