Per-folder unread counts (in the account list and the sidebar) show the unread count reported by the server (for IMAP and EWS, at least, where this is tracked server-side).
Some of those unread messages may be very old, but the information is there, and I think it's useful.
The smart folder pulls from messages actually synced to the device -- and the unread count reflects that too.
You may want to increase each account's "messages to sync" -- for the "sync window" to include more of your unread messages, hopefully all of them (except if you have some long forgotten ones).
Long press an account -> options and folders -> account options -> "messages to sync". The default is 25, 100 is still fast, 250 almost... the rest is for people who check mail a few times a day.