I'm using NMM to sort and manage mods. However after updating to the beta. Some scripted mods stopped working. After deactivating them and loading a clean save, I have found that those mods have caused my game to error up and CTD whenever you open the main menu. SO I decided to start a new game now, which is not that big a deal anyways.

So the primary question now is. Do deactivated and old mods through NMM effect your game at all? In terms of performance, stability, save corrupting and future game updates as in the example I have provided above?

It is too hard to go through the data folder and delete every file from old mods that I am no longer using or that became outdated. MY solution now if the above is not true, is to delete everything reinstall the game and just add in the mods I will be using for sure. Textures, RCRN, UI, killmove, WIS, DD, etc.

Quick edit. Almost all the mods I am talking about were installed manually and not through NMM. This may complicate things.

Wrong section for this, we've got a board for mods.

I'm a bit unfamiliar with how NMM stores files, but it's based on OBMM which uses separate files to keep track of things and only extracts them into the Data folder when you activate them in the program.

So, not really. However, it is harder to see conflicts and by deactivating mods, you need to reinstall the mods that were loaded before the deactivated ones in the list as NMM doesn't respect install order, at least it didn't last I heard.

You should try to use NMM whenever possible for just this reason. Unfortunately, the CK is so new and so many issues are being addressed by patches that this will be a common occurrence for awhile.

eta:
A good practice before updating mods is to deactivate them through NMM, run the game and make a new save, then update.