Nope, no need to do anything other than delete the directories that belong to removed jobs.
Since they've been removed from Qube, the database doesn't know anything about them anymore, and if they're not in the db, the supervisor doesn't know about them anymore, and the worker never cared once it had finished the job.
If you like, and since you're on Linux, I can set you up with a script that you can run as a cron job once or twice a day that will automatically clean out logs that are from removed jobs.