Since Google NaCl is C++, will I be able to access the file system somehow? That's pretty much needed if I am to create a game or a desktop app.
Yes, but this access is supposedly secure and only able to access a sandboxed file system. Apparently you'll be able to do mmap calls, even. What could go wrong? :-)
Beyond any data files that come with the download, additional disk quota is an "app privilege" you have to "approve" when you install something. It can range from 0 to unlimited.