There are a few places in Emerald and Ruby that are secret, you don’t have you go there, but it’s fun to and they have a few rare items too.
1) Abandoned Ship: Surf from Dewford to Slateport (you need to Surf, don’t Fly) and along the top where the rock barrier is should be a ship (the abandoned ship) there are a few trainers in there which you need to battle. After reaching the end of the ship, the scientist guy tells you he needs a Scanner. Get the Storage room key and unlock the locked door (did I mention that all the doors in the ship are unlocked except for one, that’s the storage room door). There will be a ‘Rm 1 Key’. Use Dive in one of the rooms with a patch of water and surface on the other side and will be 6 doors, about 2 will be unlocked but blocked. Unlock the Rm 1 door and there will be shining stuff (about 3-4) one of them will be a key for another door, the rest will be shiny trash. After unlocking all the doors, you will find the Scanner. Take the Scanner to Capt. Stern in Slateport (he’s in the place where you will be able to go on a ferry after beating the league) and talk to him and he offer a trade for the Scanner for either a ‘Deep Sea Scale’ (boost Clampearl’s Spe. Attack) or ‘Deep Sea Tooth’ (boosts Clampearl’s Spe. Defence). Items that can be found in the abandoned ship are Water Stone, Escape Rope and a few others. Phew, that was long.
2) Meteor Falls extension: Go in Meteor Falls (in route 115) and there will be a spot where you can surf. Surf there and there will be a waterfall (use Waterfall to get up) and there will be a new place). You will be able to find some items and there are a few trainers.
3) A cave (i 4got what it’s called): Go to Mossdeep and Surf around to the top of the land and keep surfing up. There will a cave, infront are 2 girl trainers you battle. Go in the cave and walk around. You will find an old guy who says if you find 4 sea salts and 2 shoal stones (or something like that), he will make you a Shell Bell, they can each be found daily.
4) Go to Rustboro and up to route 115 and down the stairs and there is a space to surf. surf up and there will be land, continue surfing between the rocks and you will find a place with 2 trainers, rare berries and places for a secret base.