As long as you only use cia files for online games and don't cheat on pokemon, you probably won't get banned. If you do, you can usually unban yourself.
You got this around the wrong way. You update the system, not the games. Feel free to update, hacking will still work.
Launch the R4 cartridge, wait for the menu to load, push the third button, push the top button, and then the top button again to change the language to English. I had to figure this out, because it was in Japanese for some reason.
The upgrade to boot9strap updates Luma3ds at the same time, and updating gives you:
More features
More compatibility
More stability
And more speed
You only get improvements when you update it, so you should update.
Make sure you have the latest version of Luma3DS and B9S, using https://3ds.hacks.guide/updating-b9s or https://3ds.hacks.guide/a9lh-to-b9s then launch the Luma3DS updater.
After updating B9S and Luma3DS, try going into System Settings and finding the System Update option.
You may want to remember this trick, as you might need to do this again in future. Also, your Nintendo Switch might be faster now because this also defragments the SD card, so you might want to do it occasionally. Don't do it too often, or it could reduce the life of the SD card. You probably...
It is probably just warming up because of the processors might be doing a lot of processing, the MicroSD card might be in a lot of use, and you might be using a lot of power. Luma3DS could also be increasing the processor clock speed which would generate more heat. As long as the 3DS doesn't get...