This problem is not actually linked to any mods directly (although maybe one of your mods might be making it worse). I actually had this problem before I installed my first mod. I would be wondering around the Commonwealth and suddenly my gun would disapear or I would finnish crafting stuff at a settlement and try to bring up my Pipboy to fast travel and it would not be there. Whatever the reason the game just seems to stop loading the textures. I have found two fixes that worked: 1) Just do a quicksave and reload. 2) Equip a gun with a scope and then "aim". The scope is important, guns with just sights still try to use the gun texture during the aim and won't try to reload the texture after you lower the gun. Either solution has fixed both the invisible gun and Pipboy problems for me everytime I have encountered them.
