Answers to both those questions:
1) Aqua has just been in the Realm of Darkness. It is a very large place. It is unlikely that anyone would find her there if they were not looking specifically for her. The secret ending takes place after KH2, and she's still there.
2) Terra wasn't completely screwed over - it's implied that the hearts of the original Xehanort, Terra and Eraqus were all contained within the new Xehanort's body. Now as we know, the new Xehanort eventually splits into Ansem and Xemnas, so I'm not sure what happened to them, but it can't have just been an abrupt end. We'll probably see them in some way at some point again.