Yup, they're hidden alright!

Hidden:

1. On Route 11, while surfing there is a gap upward toward the end section of the route. From there you will beat a trainer and find an island with several secret base sections, and if you find another small gap another secret base!

Secret: (need secret power)

1. There is a sign that leads to this area in route 1. It reads: "the secret lies between the mossy tree and the immediate flower".All you have to do is head back to Mossville and use secret power on the flower in the uppermost part of the town!

2. On Route 2, surf off the bridge up. Then a tree to the topright will unlock an area that needs cut to get into the grass!

3. Right when you enter Route 5, you may use secret power on the bottom trees to reaveal a windy path to a lakebed, from there you can surf to beat an old man trainer with a shiny Urich!

4. At the end of route 11right before the Clear Lake town, you are able to use strength on the bottom trees to open a path to an odd colored green tree!

5. Apparently there is a secret desert, but it still evades me...

Any other secret or hidden areas - especially the desert do share! :D