the .py script files can be edited in any word processor, such as notepad, although it does have an native editing program called IDLE that is specifically designed for this language. before you ask, you cannot edit the .pyc files, they are the compiled version of .py, and you need the source .py file. If you replace the model, you only need to change the script files in if you changed the name of the model file, the file to change that is located in the Scripts/ships folder or if the model is not the same exact scale, in which case you will need to edit the hardpoint file in the scripts/ships/hardpoints folder using either your word processor, or the MPE included in the SDK.
To answer your other question, you can also edit the models by opening them with niftools' nifskope, and exporting them to whatever program you need to use, although you shouldn't have any problems loading them in milkshape with milkshape's nif importer if you are doing it right.
But don't go off meddling with the models just yet, usually slowdowns are caused by the oversized textures most mods use, not the models. Try scaling down the textures from their current size to the next size down, if it is 2048px on a side resize it to 1024px if it's 1024px, try 512px, just make sure they stay the same ratio. I don't remember what size the nebula's use off the top of my head, but that should work.
Keep in mind that Supermod isn't really designed to be messed with, if you change the wrong thing, it won't work right.