@istanahutan Crista in Ordon uses Deku Sticks to make potion. It should've been mentioned in a quest at the beginning of the game.
If you're referring to Three Eye Rock and King's Tomb, I don't consider them mini-dungeons, just small cave secrets (and there are lots of those), so they're not listed here.
The only map is the in-game map, which should (hopefully) represent everything important. If you haven't found the map of the north, visit a town called Kasuto in the east of the northern continent.
There is a small island in the south-west of Subrosia, but nothing significant. There are small secrets in each of the graveyards, true to Zelda form :)