It seems like you have Wi-Fi enabled on the console and the Switch automatically downloads the latest system update. There is a way to delete it but before you do that, you have to remove your Wi-Fi settings otherwise it will download the system update again. To delete a pending system update, simply boot into Maintenance Mode. This is achieved by holding both volume (-) and (+) when turning the console on. You will know you're in Maintenance Mode once you a screen with 3 options. From here, you don't have to do anything as simply entering Maintenance Mode clears out any pending system updates. Just reboot your console and you're all set.
Well, the first problem is that the Nintendo folder belongs to another console so when you boot it up, it will complain that the SD card belongs to another device and will ask you to format the SD card. Other than that, it will be able to boot CFW on sysMMC. It won't be able to boot emuMMC since emuMMC is console-specific.
Maybe those apps had their GitHub apps removed or the author no longer wants them on the appstore but they forgot to update it on the site? I'm not really sure. You can always try asking in the
appstore thread. Which apps are you referring to anyways?