From my understanding after dealing with file cabinets / drag & drop recently, I would like to think the same file behavior applies to your context.
Feel free to correct me, as long the PDF files are easily accessible outside of NS for the users then its okay to remove after 1 year.
If a PDF file is used in an order then it has to be stored somewhere, so i imagine if you removed the files then they won't accessible within the transaction itself but details about the order will remain as part of its history in a similar manner to system notes.
FYI - I haven't worked with suite commerce yet, again just thinkin from a file behaviour perspective.