Automount'ed Samba Shares accessible via Command Line but hidden in Finder?
Perhaps the 'hidefromfinder' option in your auto_master setup file has something to do with it?

/net            -hosts      -nobrowse,**hidefromfinder**,nosuid
/home           auto_home   -nobrowse,**hidefromfinder**


From the auto_master(5) man page:


  The
       hidefromfinder option is used on maps that shouldn't show up as folders in the Finder; it causes the UF_HIDDEN
       flag to be set on the root directory of the map.