And like vim, you will probably never use, nor need, all the shortcuts available. I use about a dozen keys in mutt, some of which are custom binding I use to send messages to separate maildir in one keystroke.
All my emails get into my Inbox (except for bugzilla stuff). I go through my Inbox several times a day, and as I read messages, I press 'o', 'n', 'e', or 'a' to send the message in one of the four folders I mostly use. For the rest, I sort it manually using the 's' key.
This way, my Inbox is always empty. Or if it's not, I know it's a message I need to get back to later on. There's usually no more than a handful of those.
Granted, you can do that with any mail client. But mutt is particularly well suited for the job.