1. Do you have numbers on power usage? Your spinning rust drives are using 5-10 watts each. It’s likely that they’re using more individually than both Pi’s combined.
2. This is fixable with more software
3. Unfortunately a part of life with Raspberry Pi. Maybe consider swapping to an SSD?
4. This is a 12 year old Synology. I empathize though, I’m running a DS416j I bought in 2015, so almost as old.

My suggestion would be to focus on getting a better Synology with an Intel chip that can run Docker. You’ll start off being familiar with the base OS and can make your backups rock solid and you’ll be able to run whatever you want with Docker. Assuming you can swing a 4 bay NAS you’ll also have room for expansion.

Yes. Keep in mind the several ports that are plugged into the phone module (the middle module on the top set of three). You can easily turn those ports into ethernet ports by unplugging them from the telephone module and plugging them into a switch, but you’ll need more switch ports.