Hey!
Noticed same…
That when save was loaded and then activated WeMod itself after, resource mods didn’t work.
But it works if you start game via WeMod (press the “Play” button there on Stellaris page in WeMod software)
No matter if you start game launcher itself just by pressing that Play button on WeMod or if you start game launcher via Steam and start loading latest game save (by pressing “Resume”) just make sure WeMod is loading mods BEFORE save is loaded, meaning before you’re in the game session.