For most aircraft it's the textures that make it large, not the mdl file.
Referencing panels and soundsets instead of creating a new copy for each aircraft is a good way to start.
Getting rid of textures you don't use is next (do you really need a hundred textures for that Posky 747?).
Then cull aircraft you never use anyway.
Your aircraft folder as you describe it looks kinda sparse though, only 2 dozen in there?
Mine's running up into the hundreds (though most of those are AI
which are eyecandy only). FS2004 is now taking up over 20GB of diskspace, and FS2002 is still sitting there eating another 15 or so.