Solutions for the first possibility include moving the card directly to the female folder. The third, the data got corrupted at some point in transition to or from the website it was hosted on or during creation of the card itself if the card wasn't downloaded. These websites will sometimes only download the image data as if it is just an image.

The second, the card does not have the character data needed for the game to detect it and is instead just a simple image, this is a common problem with downloaded cards from websites that don't have the proper handling in place for Illusion game assets. The first, the card is not in a compatible format, like HS1 cards won't work with HS2 for example. There are three reasons this second possibility could be the case. The second, the cards are not compatible with the game and the game is not detecting them because of that.

The first, the cards are buried too deep, I noticed it can only go one subfolder deep or at least the Koikatsu version of the mod can.

So, you're saying the subfolders listed in white, when selected and turned blue like the female folder in your image, don't show any cards? There are two possibilities I can think of.