Welp. Yesterday I only removed mod folder from the stellaris documents folder, reinstalled the game and tried launching it a few times. Avast thought for a moment that the new launcher is suspicious and its action (I think the launcher tried to modify a modlist file or something else, didn't take screenshot for that) as a part of ransomware protection so I clicked the button "this action is alright". I launched the game that time and it still didn't launch the game properly (two times). I turned the PC off and I went to sleep, then in the morning I woke up and saw this.
All my mods are back on the list, but not loading in the game. There are only 2 mods in the "mods" folder.
Did the modlist for launcher change anyhow from previous launcher? Maybe it wasn't updated properly and it tried to load older one instead while crashing the game.
I unsubbed, launched
the launcher closed it and subbed again one mod that wasn't loading properly then I launched it again and did this.
Spoiler: It worked only for that one mod, and I have 3 mods in the "mods" folder xD
It seems you have to unsubscribe all mods, play the launcher (you don't have to load the game) then you close it and subscribe the mods again and play the game.
So I unsubscribed all mods, "All installed mods" is empty, meanwhile playset is still full... Reloading all mods didn't clean it so I'm removing it one by one and I'm back to the clean launcher. (Protip: Open the mods in a new tab using middle mouse button so you can easily find and resubscribe them later).
Now (probably) all the mods are back in the folder and they launch in the game.
TL;DR:
-antivirus or something probably blocked launcher from downloading mods from steam,
-unsubscribe all mods (Protip: Open the mods in a new tab using middle mouse button so you can easily find and resubscribe them later),
-open the launcher from steam,
-when you see you have no mods installed, but still have them in playlist: remove them from playlist (just to be sure)
-also I have "reloaded all mods" but I'm not sure if it did anything at all,
-close launcher,
-subscribe to all your mods and open launcher,
-load mods and play.
I hope it helps you.