For Mario Party Jamboree, and Kirby and the Forgotten Land they are including additional content (a bit like adding Bowser's Fury or Lanky Kong). For the Zeldas they are adding second screen features.
I don't like the up sell but it is offering something, I can see them feeling they have a justification for the fee there.
Really I'm surprised they are offering the upgrade licences as cards they can sell in 3rd party stores, hopefully we see some competition there.
Edit:
The Nintendo published games receiving free updates are listed here:
Their emulators have always been proprietary. The waters were a little muddied by the NES/SNES Classic consoles using a Linux OS but the emulators were their own code.
Their FOSS code is made available when required and is published here:
https://support.nintendo.com/jp/oss/index.html