It will yeah, although with modern SSDs it really isn’t a big problem. I’ve used an Samsung 840 EVO as L2ARC for 8 years now.

Try changing to another upstream DNS server in Adguard (such as https://dns.cloudflare.com/dns-query) and see if the problem gets resolved?

Always had trouble with Nextcloud but ever since deplying it on NixOS it’s been rock solid. Both performance and reliability.

Personally I would go for ZFS with the SSD as a L2ARC. But among the options you listed I would do BTRFS RAID1 if you’re only gonna use two HDDs, and MDADM RAID5 with XFS if using three.