I've started setting up my media server and was wondering if I should put my docker containers with sonarr and radarr behind my VPN the same as my qbit?
I mean you do you, but there’s always a trade off with these types of things (usually security at the expense of usability), so most people would be better served by taking stock of their activities, the risk caused by those activities, then mitigating that risk to an acceptable level. If acceptable to you is cruising around to mcdonald’s parking lots so you can bounce off their wifi like you’re taking the risk of ordering weight more power to you, but just know that from a risk mitigation perspective you’re implementing controls way out of line with the actual risk. Probably, depending on your local laws etc idk i’m not you.
It change your public IP, so when you swap server the services you use will see another IP from you, if you swap server constantly supposing someone it's trying to find out where you are they will have a list of different places and it will make it harder to know where you really are so they will desist using the IP method.
There is a variety of measures you have to take to be secure, swapping servers it's just one of them.