I have a similar setup using Truenas to store data. I’ve setup a VM in Truenas that can access the data via NFS (easier to setup on Linux than SMB).
It’s nice to keep all your services contained in one machine, as long as it has enough resources, and will probably consume less power than running another PC.
I use qbittorrent, most people seem to agree it performs better than Transmission. It’s accessible from a web interface.
RAID5 is risky on drives that large, there’s a decent chance of a read error during a rebuild.
RAID6 will provide more protection but you lose two drives worth of capacity to the parity data. I’m not sure if a three drive RAID6 is actually possible but a three way mirror would be more sensible as you’ll avoid the extra computation of parity calculation.
Imo RAID6 starts to make sense in an array of 5 or more drives.
That might explain the problem. Assuming adguard returns an nxdomain for blocked sites then the devices will try with their secondary DNS server and get to the blocked site