Yeah, I did it like thousand times before - didn't work.
Anyway, I think I found a culprit although it's still a mystery.
I totally disabled Meshes folder and CK was working again!
My Meshes folder is more than 1Gb so it's not possible to check all meshes.

I backtracked my steps and found that the problem is furniture/noble folder. I made a full replacer for noble furniture in Enderal so it looked as less Skyrim as possible, and in game it worked fine for quite a long time.
What is interesting, that I checked and re-checked EVERY mesh by opening it in CK (right mouse click) and ALL of them are opening normally.
When I disable the whole folder with furniture - CK is working again! If I enable furniture folder - CK crashes.
So CK is able to load all my meshes separately but for some reason it doesn't like the folder with all those meshes and crashes on loading it. Mystery.
Oh, well, I can live with that.

Will disable a furniture folder while modding in CK and enable it for playing.
Just so glad I finally was able to solve the problem!

Hope it will be the end of my battle with CK and I'll be able to make mods for Enderal again!