As smallg said "most files should be encrypted". The files in your standalone will all have the prefix "_e_" added to their names to indicate that they are encrypted. One exception is that .ogg audio files do not seem to get encrypted, while .wav's do. Users will be able to see all your files, but not be able to do much with them.
I'm not sure why they can't pack all the resources into the .exe, but most games leave all their files "hanging out" anyway.
Windows 10 Home 64-bit / Intel i5 2500k @ 4.4Ghz + Asetek 510LC / Intel DP67DE / Intel 530 Series 240GB SSD / 12GB Kingston KVR 1333 / XFX Radeon R9 285 / Corsair TX 650 / Antec 300