AoF and FF1+2 CDs are hard to find because most ppl think they're better than the cart versions. They're cheaper, contain the same stuff and don't have unbearable load times except for a couple of secs to boot up the game, so ppl tend to keep them.
Then there are some who buy Neo CDs as sound track albums. Some of the original NGCD games are cheaper than their official OST/AST CDs, which also takes away many copies from the market. This situation gets worse if we're talking about a game which never got an official soundtrack release (for ex. the Slugs).
However, they're not rare if we're speaking about release numbers. They have been released in slightly lower quantities compared to CD releases from 1995/96, but that alone can't be the reason why they're harder to find than other games.
FFS and specially AoF2 aren't rare at all.