1. Get latest nikke mod manager
https://gamebanana.com/tools/16887

2. Open it and set it up (selecting your nikke game path etc)

3. Download the repacked mods
https://mega.nz/folder/D8R2HCjK#1jxV5LqXItgtnXbiKPhsKw/folder/S1g1XTAY
This is the key thing that made them stop working, the mods all had to be repacked in a certain way to start working again, if you use the old ones they will not work. You could probably do this yourself but someone on the blacked modding discord (https://discord.gg/WsdMhZNnSp) repacked all of the known ones already. If any future ones come out you may just have to hope the maker does it properly.

4. Extract and put the mods in the "mods" folder in your nikke mod manager path

5. Launch the game wait until the game gets to the "Touch to start" screen, then boot up the nikke mod manager

6. In nikke mod manager, Activate All and then Apply all mods. You have to do this in the touch to start screen.

6. Start the game and they are hopefully working!

*NOTE: This game is pretty volatile to mod it seems so I can't promise any of this will always work but that's what I'm doing now.  It usually works on the first boot but if you close the game and try to do it again (as the mods have to reapplied every time) it tends to bug out and either have a blank screen in the lobby or just not load properly so you may just have to trial and error it.

Also updates tend to break the mod manager so if there was a recent update you should first check to make sure you're using the latest version (duh).  There may be times where you simply have to wait on it to be updated again.