Hi I had problem, when I had 40 Gbytes large mail folder. It was caused by the large account files.
If you use time machine and all your accounts are imap, backup and erase all your accounts.
Now recreate them, but don't forget, mail folders which are set to save on the mac and not on the gmail imap server will be deleted (you could create new folder and by dragging from the mail app to this one to copy them).
It saved me about 39 Gbytes of garbage space (not necessery and created by some erorr in the Mail client.