1. The majority of the people so that they can't just navigate to the folders of resources and freely take whatever they want.
Majority of people just don't care.
2. Many assets you purchase require that you protect them with at least a basic layer of a password protected file or similar.
I've never heard of that. Can you link me to some of such asset sales or requirements?
You are conflating two features (security and packing) here. You can encrypt files without packing them and pack them without encrypting them (or do both at once in various ways or neither).
If you want just single file packages then use physfs or sqlite3 directly. They are easy enough to use as is and there probably are C++ libraries for them too. With how SFML's policy on stuff like that is it's really unlikely that it'll ever be integrated in any way.
If you want some actual encryption too then you can try use some encrypted archive format or encrypt and decrypt individual files or pieces of data (from folders, zips, sqlite3 - wherever) yourself with AES or something that but if the key is in exe it'll be really easy to get it out anyway and it's a performance hit compared to just compression and reading data from disk.
Many games actually do use many files organized into folders. Some also use zip (older id tech games, Love2D) or some other special purpose but non-obfuscated format for which tools exists to work with totally freely (like grp, wad, swf, ktex, unr/utx/uax/u**) and it's just an organizational and/or performance thing, not obfuscation or security feature.
Tons of engines and games use packages but the only engine off the top of my head I know of that has actual encryption is Irrlicht (it has AES for zips).