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Use bind mounts instead of docker volumes. Then you just have normal directories to back up, the same as you would anything else.
In general, it's not a problem to back up files while the container is running. The exception to this is databases. To have reliable database backups, you need to stop the container (or quiesce/pause the database if it supports it) before backing up the raw database files (including SQLite).
Exactly the reason why i always exchange the volumes in any compose file with bind mounts.
Also you don‘t have the provlem of many dangling volumes
This is your answer. It also has the benefit of allowing you to have a nice folder structure for your Docker setup, where you have a folder for each service holding the corresponding compose yaml and data folder(s)
Rsync works fine for most data. (I use borgbackup) For any database data, create a dump using pg_dump or mysqldump or whatever. Then backup the dump and all other volumes but exclude the db volume.
In general there is no problem in rsync'ing the volume bind directory. But that depends on the application, which is running in the container. I. e. you should not copy the files of a running database. It may corrupt the data while it's being written.