The multiple package "extensions" are created when you install a sims2pack with clean installer and choose not to install into the default directory. The more people have done that before to that particular file, the longer the filename. Some people delete the "packages", but not everyone bothers (or knows).
It doesn't have to do with duplicate files, though. But still it's a good idea to check your downloads with clean installer every now and then for duplicates.
Will the end sim I downloaded use the original file already in my game, if I don't use the one that came with the sim with the name they assigned in the sim package?
Yes.
When I install sims, I look over the names of the custom content. The most popular are already in my game and I know them by now. So I unclick them, because I know I already have them. The Clean installer asks to overwrite files, if they are already in the downloads folder. But if one has sorted ones stuff neatly in subfolders, duplicates ensue.