When I run the decompiler of the traffictool addon, it creates aircraft.txt which doesn't contain all the aircraft I have on the aircraft folder. What am I doing wrong?

That is normal! It just means you haven't either manually added them to the list or used AITM - http://www.molitor-home.de/FS/AITM or yRoute - http://www.spacejock.com/ to add them.