Hidden in what sense?
On Linux, files whose name start with a period are "hidden" (by convention, many commands ignore them)
On OS X, files and directories that are hidden to the Finder have a special attribute in the file system. I don't think there's an accessor for that in Pharo yet, but as a workaround you can use the system command GetFileInfo to check the state of the invisibility flag (v):
GetFileInfo -a v /Applications
# should echo 0 (invisibility flag not set)
GetFileInfo -a v /bin
# should echo 1