Regardless of how you host Nextcloud, what you described is one thing I really like about Nextcloud: the major part of it being synced to several devices. As long as you have a computer with the desktop client that's on every once in a while, your stuff is saved across different devices.
I've had a similar thing happen once btw, deleted the wrong server. It was "just" monitoring data, but I had spent a lot of effort building it properly. I eventually started over it, but knowing the whole thing is gone feels really bad.
Your CPU should be perfectly capable of that. I ran Proxmox with some VMs and containers on an i5-2400 with 16GB RAM just fine.
You could run on bare Debian as well but virtualization will give you more flexibility. If you get a Zigbee Dongle or the like, you can pass it through to the VM Home Assistant is running in.
I don't know MergeFS but usually the recommendation is ZFS.