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Basically the files in your data folder match the filesizes of the files in your NMM mod folders, as such it mirrors the filesize increase that your NMM files create but doesn't actually increase the overall size useage of your hard drive due to how windows handles hardlinks. For example, if you uninstall a mod in NMM the size used on the disk as a whole will only decrese by the size of the mod in the NMM folder for it and at the same time the filesize of your SSE directory will also shrink by the same exact amount.
A good readup on the differences between the different link types in windows is here: https://superuser.com/questions/67870/what-is-the-difference-between-ntfs-hard-links-and-directory-junctions
The only real way to save space would be to unpack the files, pull the textures out, repack them into a single mod, then delete the 2 mods and only use your new custom mod instead. This is actually not that difficult to do, but it's very time consuming and you could completely wreck your build if you screw up. Like anything else though, the more you do it the faster you get it done.
Just keep in mind that a lot of the replacers, for instance Immersive Weapons or Immersive Armors, are large files. The same goes for something like Noble Skyrim. The base game itself consists of mostly textures, meshes etc etc and that's what makes it a nice sized download. When you install something that replaces those textures, you aren't replacing them in the download, so you're doubling the size of them. Even more if you go for 4k/8k textures.
For reference, my mods folder for MO2 is 40.4 GB, and I don't have a lot of texture replacers. That is Noble Skyrim (2k textures), SMIM, and a couple others plus a lot of armor/weapon files. 33GB is not much at all.
Titile: "HELP! Skyrim won't load. Instant CTD! Did new patch break my save?"
Body: "I have lots of mods, but I wanted to save some space so I deleted things that didn't really look important. They all work fine, it's just the game won't start anymore. Has anyone had a similar problem? Using NMM if it helps. I really don't want to reinstall everything, so please don't just say that. That's not a valid answer for me."
Well, yeah, maybe you are right. I will leave things as they are. No purpose of breaking the game for some disc space. I still believe mods taking so much extra space is annoying, but I will still rather use NMM than installing mods manually.
Granted, there's a lot of modding-related work files but still, the more you play and mod, the more you'll get stuff. It's normal.
There's people with over a thousand mods merged together so breaking 100GB loads shouldn't be anything extraordinary. Don't worry about it and just keep cramming more to your game, Special Edition can handle it. If running out of disk space, buy more!
Those extra games eat up ~40GB in total and should I run out of space, I'll just get rid of some of them. The few Steam games on the SSD are on my top playlist and all the rest are dumped to a HDD. Priorities set right.
Been thinking about getting an extra 500GB SSD but as long as I can download and edit stuff for Skyrim using the current setup, it's fine. Still some 40GB free space and another 40GB from those games if need be... so time to head back to Nexus.
indeed then mod further to fix it.