First I was
-available at or near the beginning of the game?

Then I wasn't
-unavailable for a little while

Then I am, and then I am, and then I am
-the available again, in disc 1, still available in disc 2, then still again in disc 3

Hidden secrets, and I still am
-maybe where it's still available is hidden?

But not as much
-some of the places it can be obtained have been closed off?

Hmm... No guesses here, but that's how I analyzed it.