Long story short, I did “rm -rf” my system but luckily I was using btrfs-limine and restored my system files with snapper. Since it didn’t create snapshots of @home, every file inside of it including folders themselves are deleted. The lost files weren’t that important anyways but my folders are missing so what steps should I take from this point, using mkdir and creating home, desktop, documents etc. is enough or should I do something else?
Run
xdg-user-dirs-update
It will generate all new ~ user directories.
LOL. This surely a wind-up.
I sure hope so. “Accidentally” inputting a widely-known deadly code would be kinda stupid. 
Last time I did it, was in college and I did some wild pattern match that ended up being rm -rf / (though it was written much more confusingly…I thought I was being smart). It happens ;0
I was deleting some files on a disk I used to use with windows, which was ntfs3 and gui delete was giving errors sometimes so with my brilliant and lazy idea I just direct the path with CD and rm -rf * the whole folder, after I did it 5-6 times I was kinda on auto-pilot and realised too late that last time I used it CD didn’t direct it to a folder, maybe because special characters idk, that nuked my system in 6 whopping seconds somehow sadly. 
Default config files for user home directories are always located at /etc/skel on Linux.
You can copy them from there to your home directory.
It happens; I deleted my entire lightroom catalog for the past 7 years by accidentally forgetting a / when pushing a directory update
Mine is empty, does that mean something?
Yes. It should not be empty.
The most likely explanation is that your rm -rf deleted it, and the snapper restore did not restore it.
/home is not the only subvolume excluded from snapshots. Although I’m a bit surprised /etc/skel would not be included in a snapshot, I don’t see any good reason for that.
In any case, it’s very likely you have other files missing as well.
I would recommend a full reinstall tbh. A wild rm -rf / is a pretty catastrophic event, and snapshots aren’t really meant for recovering from that, just rolling back the clock on updates, installs or system config changes.