How can I tell if a directory has APFS Fast Directory Sizing enabled?
We now know the previous answer is a bit off since Apple has recently released more technical details on APFS.  Fast directory sizing is indeed enabled on a per-directory basis and this can be checked by the user (albeit not easily). It can only be enabled when a directory is empty and must also be turned on for every new subdirectory as well. Details: https://developer.apple.com/support/apple-file-system/Apple-File-System-Reference.pdf

Relevant quote 


  You cannot enable Fast Directory Sizing on directories containing files or other directories directly; you must instead first create a new directory, enable fast directory sizing on it, and then move the contents of the existing directory to the new directory


We now know that you must set this flag to enable FDS


  INODE_MAINTAIN_DIR_STATS: The inode tracks the size of all of its children


Though still unclear to me if macOS is turning this flag on automatically where appropriate or not, but some initial experimentation makes me think it isn't being used yet. I assume it will be used in forthcoming macOS updates.