Settings -> Software Update or something like that. You can also set it to auto-apply. Mostly, I ignore the popup and run dnf update -y && snap refresh && flatpak update -y as root every once in a while when I think about it.

1. Nah. Set the frequency to weekly or monthly or something you don't need to do daily. I do monthly.
2. Yeah, there's a lot of updates and that's a good thing
3. Probably
4. Yes

Setting up a watchdog and crash kernel might help or let you diagnose it

Take a look at https://diskprices.com/ for the best price per TB. Backblaze has been pretty great about sharing their hardware specs and builds. Maybe get some ideas from them https://www.backblaze.com/blog/open-source-data-storage-server/

Why not a tor relay? If you're not an exit it is pretty darn safe. How about a tor snowflake proxy too? Even easier and safer.