I have a hard time calling any Final Fantasy a cult classic it sold millions on release.
On release? The first couple FFs actually sold less than a million each. The series didn't become million-seller until III, and only in Japan of course. The first game to reach 2 million was V. The first game to sell over a million and multiple million outside Japan was VII.
Now that I'm done being pedantic, IX gets called a cult classic sometimes despite selling a little over 5 million copies worldwide because 1. that's quite a bit less than VII, VIII, and X around it which each sold something around 8 million, and 2. the sales for those games were also more evenly split across regions, whereas over half of IX's sales were in Japan alone, and supposedly it didn't even break a million sales in Europe + rest of the world (outside America & Japan). IX sold less than VII and VIII in Japan, but it still ended up as the 4th best-selling PS1 game there behind those and DQ7. It was significantly less popular in the rest of the world, in fact it may not have even particularly much more than other non-FF RPGs Square was releasing. It suffered from a combination of timing (PS2 had just come out, so some people weren't really paying attention to new PS1 games anymore) and the tone and artstyle of the game being so much of a departure from VII and VIII (which is what most non-Japanese fans only knew the series for).
So while FF9 might not be a super obscure game in the grand scheme of things, it has so much less cultural presence in the zeitgeist than VII, VIII, and X that it's understandable that it's viewed by some as fitting the description of a hidden gem.
On an aside, V also gets called a cult classic sometimes, which is understandable since it didn't originally come out outside Japan (and would have been back before FF was popular outside Japan even if it did), so only big FF fans and those going back to play an old, early-90s RPG (not actually that huge a group compared to the general normalfag audience) have played it.