Are we talking similarly to how the Wii runs n64 at 480p60 without a hitch? If so then probably. The problem is that the emulation isn't very good. Most games have small effects missing. For example in Mario 64, noise isn't implemented so when warping or using a vanish cap you are missing an effect. The emulators are heavily hacked per game too, look at any Wii n64 injection compatibility list.
https://wiki.gbatemp.net/wiki/VCInjections_Compatiblity_List#Nintendo_64
As for running dolphin on switch, AFAIK our graphics drivers nor dolphins arm64 jit are as fast as they could be. I'd imagine at least lightweight games could be playable eventually without per game hacks.
Getting usable code from a compiled binary is not an easy feat. If you had the code you could use some of it but if you used any quirks of the original system things get much harder. From what I understand the 3ds's pica GPU is quite weird to the point you couldn't reuse much rendering code at all. Also, about your example for conversion
Unless I'm unaware of some programming term, this is just audio conversion. They presumably convert a .wav or similar standard file to one of those formats. If they have the code to do that, it wouldn't be too hard for a large game company to make code to reverse the process and then redo the conversion for the new format.