JavaScript shouldn't have any restrictions on opening or saving word documents. You should be able to do so using Sys.OleObject ('Word.Application') I believe.
PDF files, in general, are going to be tricky to work with because of their nature but there are methods of doing so as well.
Generally speaking, though, TestComplete can interact with the dialogs within any application so opening Word and selecting "Save As" is a means as well.
Can you post what you have attempted to date?
Also, I'm curious where you read that JavaScript can't open or save documents.