They could add a second FIRM update path that isn't currently patched by CFW in order to replace the B9S FIRM with original FIRM. This would cause affected systems to be reverted back to stock.
1. I was referring to the FIRM partition in CTR NAND.
The 2DS XL was announced before we had b9s so it was probably too late in the development cycle to alter the design.
They can't start altering user's personal data. I don't know if it is illegal or not but it would cause a public relations nightmare. It just isn't done.
It would have impacted the stability.
"boot.firm" isn't necessarily personal data. They can easily claim that they detected it as malware (as most anti-virus vendors do with regards to keygens etc).
It isn't the legal side that they'd be worried about. It would be people being outraged and causing a public relations nightmare. Nobody wants to think that they could put personal pictures or documents on their SD card and have Nintendo look at them or delete them or modify them. Even if that isn't the case, general users won't understand Nintendo is only modifying one particular file to slow down hackers. Facts won't get in the way of a good uninformed media beat-up.
Hasn't been a problem for Microsoft. (Windows 10 Telemetry, Windows 10 intentionally installing broken drivers, Microsoft themselves going through users' emails without consent, etc.)
Edit: @jupitteer is right. None of the things you mentioned involved modifying user data.
