Are you on the surface?
Because, really, it's kind of hard for your crew to load the outboard torps into the boat underwater unless they have gills
Also, even when on the surface, shoving eels into the boat from outboard storage is going to take a lot longer. Basically, they have to shove the big eels down a small hatch and get them to where you want them. Best advice I can give, based on year of experience, is to load the externals as soon as you have room and you are in an area where you don't have to worry about planes or destroyers coming by.