All my magic items are empty, got about 10 different soul gems filled, yet when i press T to refill my item, well absolutly nothing happens like if the key wasn't even recognized.
Anyone else has this issue or have a way to go around it?

To me what you've described happens with only some weapons, like the Drainspell Bow. With others the option to recharge sometimes is not available at all and doesn't even display the recharge hotkey on the bottom of the screen.

have you chainged your Default Wait Key From T ? if so press the key you assigned to wait & it should work

No.