Gmail's IMAP is unfortunately broken; they implement labels as folders, not tags. This means that the same message in "All Mail", "Inbox", and "Notifications" are three different messages that happen to have the exact same content and almost identical headers/metadata.

So, by default, you're going to be storing multiple copies of each message. It's not a difficult task to use hardlinks instead if you want, but mutt can't make this judgement by itself, because not all of the metadata is identical, and mutt is designed for the general case, not specifically for Gmail.

Note that this is a Gmail issue, not strictly a mutt issue; other IMAP providers don't all have this awkward behavior.