I recently got Phantom Liberty DLC and got the charged projectile launcher perk. Since I have gotten this my charged projectile launcher shot no longer has explosion visual effects. The default shot still does have the effects.
EDIT: Reinstalled the game seemed to fix it.
This was a save I started prior to 2.01 and before I had the DLC.
If you say you can see it I wonder if that mod inadvertently disabled the effects for the launcher as well. I will try to verify the game files tonight.