I have seen various mods which add weapon versions of existing items like the scythe, shovel, or various pieces of silverware to the game. To make these, it looks like a copy of the mesh was made and moved so that it would be held properly by the player. I am wondering whether this can be done in a program like 3ds max or blender, or if it can only be done in NifSkope.

Yes, it can be done and you can use Nifskope to alter it's position. I use, shovels, picks and rakes for weapon ready/tools for the sverfniblin in Underdark mod. Use CS to create your new weapon, assign the mesh and then use Nifskope to alter it's position. This will take quite a bit of practice to orient the mesh to the desired position