I'm really funny about losing track of my fish because of that exact thing. If one of my fish goes missing for more than a day, I dont mind digging a little bit, or putting a hose or something into a crack in wherever theyre hiding to cause a bit of a disturbance. More often than not when they vanish, they're just in a random hiding mode and will pop out, but of course if it's worse case scenario I always feel better off having the dead guy out of the tank rather than in it.
Could be however that the goby died and the shrimp dragged it into hiding to dispose of it (eat it). I doubt the pistol would have been the cause of death... but I'm pretty sure all shrimp are fairly opportunistic feeders, and a pistol isnt opposed to doing a little bit of hard work.