If you have a bunch of mods installed and have a problem with some of them not appearing, follow these simple steps to get them to work again.

1. Too many mods
In this case, try going to Workshop>Browse>Subscribed Items, where you'll see all your subbed mods. Unsub from a few and go about your day. 50 is the max mod limit, I believe.

2. .disabled files are clogging up the Mods folder
Go to Computer/Local Disk/ProgramFilesx86/Steam/Steamapps/Common/Cortex Command. Here, you'll find all your mods. Select every file that ends in .disabled, and delete them. This should definitely help your mod problem AND free up space - I recently cleaned out 24 Disabled mod files, worth 91 MB of space. Even if you don't disable mods, these .disabled files commonly pop up after updates. Remember to clean out your Recycle Bin afterwards!

3. Re-activate the mod in the ingame Mod Manager
Sometimes, you disable a mod here and have to enable it. Easy enough. This is also where you activate Scripts for gameplay use.

4. Re-subscribing doesn't work
You cannot simply unsubscribe and resubscribe in a single go.
You have to:
A. unsubscribe
B. load up Cortex Command, all the way
C. close Cortex Command after it's loaded
D. go back to the workshop and resubscribe
E. Reload Cortex Command after a minute or so
This usually works.

5. Mod won't download from the Steam Workshop
Either try Solution 4, or check your internet connection. Either that, or wait. You can also try going to Steam's Downloads and forcing Cortex Command's Workshop Update to Download Now.