As I looked into the keyboard shortcuts a bit more, I did confirm that Cmd-M is the OS X standard shortcut for minimizing a window. I did not remember it since I do not normally use the keyboard to do that. Upon further investigation, I did not have any luck using the Hatari keyboard shortcuts for: Insert Disk A (Shift-Cmd-A), Insert Disk B (Shift-Cmd-B), Create blank floppy (Shift-Cmd-V), or Load Config (Cmd-O). The Shift-Cmd-A starts the video recording and Cmd-O brings up the F12 SDL menu. The other keys simply are passed to the ST and I hear the default clicking sound.
However, all of the options work if I select them from the menu. The video recording does not appear to work, but that could be the fact that I did not build Hatari with the libpng framework and Hatari does not find the libpng library that is part of the open source XQuartz project.
I tried running Jerome's version to see if the same things happened to me there. However, I got the same "To open "Hatari", you need to install X11" message that I saw mentioned on atari-forum. Since I have XQuartz installed, it does not seem to think that is good enough. In 10.8, you do not have the option of installing Apple's X11 anymore.
Bob C