I'll respond to the other stuff in a little while, because I'm pretty busy today. But since this is quick, I'll do this now.
Does GodMode9 actually have any sort of nand backup/restore?
If it does, it's hidden. Learning some niche homebrew app on a dying platform in no way would make me better off. I'll stick with HourGlass9 for my nand backup/restore needs, no reason not to.
Literally on the first screen, it's the home button and then "more...". Pic under the spoiler. To restore it, you navigate to your nand.bin, and then select it with the a button and choose "restore nand backup". If you're still confused,
the guide has a page all about it.
Second, godmode9 isn't niche. It's literally THE tool for nand backups and decryption, and it's replacing decrypt9 completely. Hourglass9 development might die out too in favor of gm9, you never know. Besides, gm9 has many more features and capabilities than either decrypt9 or hg9, plus the added convenience of file browsing, hex editing, and oodles more.
Finally, the 3ds is hardly a dying platform now. Ninty's about to drop the new 2ds, and now that Sighax is out, we've pretty much unlocked the full potential of the systems. If anything, this is practically the peak of the 3ds homebrew wise, with far too many new homebrew project threads starting for me to even keep track of.
Tl;dr: it's super easy to backup/restore nand and instructions for common gm9 tasks are on the guide, gm9 is the new main decryption tool over d9 and it might even replace hg9 at some point, and we've just unlocked practically all the potential of the 3ds with more to come so it's hardly dying.
Also just FYI for other people reading this thread, if you need help extremely badly, it's better to pm me since I'll be able to respond more frequently there due to projects/life getting in the way