I'm not sure why they're not showing up even if they're in subfolders in the Mods folder
\Documents\Electronic Arts\The Sims 4\Mods\Hair - for example.
You could try moving your full mods folder w/all subfolder inside out to your desktop. This is for backup and testing purposes. Delete the localthumbcache.package file from The Sims 4 folder, in the Documents folder. - [\Documents\Electronic Arts\The Sims 4]
Add back in one subfolder at a time, load up the game to check if it shows up in-game. Quit without saving. Delete the the localthbcache.package. Repeat this step till you have it all installed/showing in-game.
If you find that some isn't installing/showing in-game, check the last subfolder you added back. You may need to delete the CC that aren't showing.