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.