This seems unlikely. I could see a couple of remasters (Metroid: Samus Returns, Link Between Worlds or Kid Icarus all seem likely to return one day), but ’will the library be 3DS games’ seems hyperbolic to me. I doubt Switch 2 will see as many 3DS games as the Switch saw WiiU games, if only that the latter seemed like a really obvious use of games much of the Switch audience had either not seen or bought first time around.
Totally okay with that. And to be honest the three games you mention are absolutely all I need personally, although I can also see something like Todomachi coming out in HD as it happened for miitopia.
If they make a Super Mario 3D All-Star 2, or a deluxe version of Super Mario 3D all Star, I can also see them bring out Super Mario 3D Land in addition to Galaxy 2.
However, having replayed 3D Land recently, 3D integration looks like a nightmare for a future port, because when you turn it off or when you play 2DS, the depth is catastrophic.
I think they'll use a mix of ports / remasters from GC, Wii, and 3DS, and remakes from older generations. We've already seen this strategy in motion the last few years with Kirby's Return to Dream Land, Luigi's Mansion 2 HD, the Mario RPG remake, etc.
For the Wii and GameCube they also have the possibility to make fairly fast ports thanks to the HD emulation technology they have developed.
But again, I think the number of potentially affected games is limited. And the games in question have been in the conversation for a while: Metroid Prime 2 and 3, Luigi’s Mansion, Starfox, F-Zero, Donkey Kong Country returns, Galaxy 2. I don’t see many other examples of first party games that deserve an HD port.
If we get this half dozen games it will already be fine. And that will certainly be enough to help fuel the pace of Nintendo’s releases.