That would be your best bet if you need to protect files that you need to be able to open and edit.
There are several file managers, including GoodReader, that will allow you to password protect files and/or folders. That only works inside the app though, so you would not be able to edit the file. You would be able to view it though. I believe GoodReader supports viewing Numbers files, but if it does not you can always export them as PDF.