@TheForestBabe
This sounds like the game is not reading the resource.cfg file. What does yours look like? I have all my mods and CC in subfolders. Most are two and three folders deep. Everything shows and the game runs fine. I have around 2,700 files at just over 5GB. It only takes my game about 2 minutes to load into a lot. My resource.cfg file looks like this:
Priority 500
PackedFile *.package
PackedFile */*.package
PackedFile */*/*.package
PackedFile */*/*/*.package
PackedFile */*/*/*/*.package
PackedFile */*/*/*/*/*.package
With this file, I can go as deep as 5 subfolders and the game runs fine.
Another thing it could be is a few broken files or files that conflict with each other (default replacements mostly) that the game keeps trying to read when loading. I suggest you go through your CC to make sure everything actually works and you do not have conflicting default replacements. One way to do that is to use Sims 4 Studio to look at every file. With that program, you can view each item on a 3D model however, default replacements will not give you a visual. Those will need to be looked at, one at the time in CAS. When I last did that, I found a number of files that were broken and had never shown up in the game. I also removed a lot of things that I thought were neat when I downloaded them but then never used. After removing the broken files and the stuff I never used, I found that my game ran a lot smoother and loaded faster. It will take a while to go though as much as you have but I think it might be worth it to you to make the effort.
Hope this helps.