I haven't looked at the code yet, and probably won't (ENOTIME), but it almost sounds to me like it's not pruning it's list of handled messages and has to walk all of them each time. I would have expected queue handling to get faster as the queue got smaller due to fewer files in the directory that it needs to search through. Maybe it's just a function of the python datastructure being used.
If it's using files as the queue mechanism, then deleting a file simply marks the entry in the directory as "available", and it still takes just at long to scan the directory afterwards as it did before.
This is a known problem with many MTAs handling large amounts of messages, and is one reason why you should use a hashed directory scheme for your mail queue (a la postfix), or you should periodically stop the MTA, move the mail queue directory aside, create a new mail queue directory (with appropriate ownership and permissions), then move what messages may remain from the old queue back into the new one (or fire up queue runners to clear the old queue while the new one is being used for new mail).
Mailman could very easily be suffering from the same sort of problem -- once you get a directory with a large number of entries in it, it takes a long time to scan it even if there are only a few files that are currently visible. Same problem, perhaps the same solution?
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