Not really CK related, but I just extracted the BSA file from a mod using the TesModManager (upgrade of OBMM) which I have used before, extracting files for skyrim with success. However, after this latest operation, I went into the data folder to check the extracted files, but noticed that most esm and esp files were missing.. The Skyrim.esm is not there...

The only files left are:

SkyMoMod.esm
SkyMoMod_lists.esp
Sounds of Skyrim - Dungeons
Sounds of Skyrim - Environment
+ONE of my personal mod files (the only one of them I currently had active. EVERYTHING else in the form of esp or esm file are gone....

Okay, I'm editing this one the go here.. I just noticed the missing files are still there, in the form of "ghost files"... What is going on here?

What is a "ghost file"n this context?

I think he means hidden files? They look ghostly in the windows file directory if you're set to show them.

No, I mean this:

Example: "Dwemer_Skyship_v1.esp" has been changed to "Dwemer_Skyship_v1.esp.ghost"

It seems only to have happened to in-active files (with the exception of the Skyrim.esm and the update.esm)

"Ghosting" is a Wrye Bash thing, so presuming you're using that. It is a way to hide inactive files to avoid the max file # limit.
Open Bash and uncheck Auto-ghosting should return them to normal.

I just removed the .ghost extension and everything became normal again. Weirdly enough, I don't think I was using WRyeBash..

Perhaps that TESModManager program is also doing the ghost file thing.

Thing is, ghosting is not really necessary for Skyrim. Even under the most ridiculous of conditions I doubt you could have someone with 509+ esm/esp files in the folder. Ghosting is a relic from pre-Skyrim days.

Doesn't it still load those files into the memory though? I have BSTamriel.esm laying around in my data folder and I don't want those 200megs in my RAM when it's not needed.

No, it doesn't, and never has loaded those files into memory. All the engine ever does is check it and move on. Only active mods are actually loaded into the game.