The first two images are from IGN and show the locations of caves and forest dwellings.
Some of these locations are found in the story. If you visit the IGN map (http://www.ign.com/maps/ni-no-kuni-wrath-of-the-white-witch/world), you can filter for the locations and then select the bubble to determine whether or not it is found in the story.
This image was posted on a Japanese website, but is incomplete.
The red triangles indicate secluded areas that you will encounter during the story. As long as you play through the story and side quests you will not need to search for these. There is also a region, south of Ding Dong Dell, that only opens once finishing the main story.
The purple triangles indicate the locations of secluded areas that are not linked to any quest and are only found accidentally or with a systematic search (or with a map like this).
The colored letters indicate locations of regenerating items (the sparkly star spots), such as flora and spring water, and can be disregarded for your purposes.
Map from: http://dswiipspwikips3.jp/ninokuni/map.html