Compacting a folder frees wasted space but the main reason to do it regularly is because it's a type of preventative maintenance. Compressing/zipping only changes how data is stored compacting changes the actual data.
"Compacting" a folder has nothing to do with compressing or zipping a file. When you empty the trash it physically removes (expunges) the messages in the Trash folder. Messages in a Trash folder aren't actually deleted messages, when you delete a message in a POP account it copies the message to the Trash folder and then deletes the original. This is a tradeoff done to improve performance in large folders. They are not physically removed until you "compact" the folder. Instead they are marked for deletion and hidden from view.
Even emptying the Trash does not get rid of them. When you delete messages in an email client such as Thunderbird they aren't physically deleted. This article was written for Thunderbird but also applies to Mozilla Suite / SeaMonkey (though some menu sequences may differ).
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