Currently MC has limited m4a/mp4 tag reading support. It can read a few basic tags (at least: Artist, Album, Comment, Track Number, Genre, Composer) and not write any. AFAIK, embedded cover art is not supported.
If you have installed QuickTime, MC uses it for decoding m4a/ALAC. Some important features like Replay Gain, Internal volume, DSP, file converter and visualizations are not available with QT decoding.
It is possible to install
DSP-Worx ALAC DirectShow filter. If the DirectShow chain is properly configured it should be able to decode ALAC files (it works for me with FDDShow & Haali splitter). This makes possible to use many of the features that are not available with QT, but it does not add support for embedded cover art.
However, even with DirectShow decoding ALAC does not behave as well as the internally decoded formats. For example, importing, analyzing and starting playback are slower than usual.
If you want to show cover art with ALAC files you could save the cover art images in the audio file folders.
Mp3tag can mass extract embedded cover images to the file folders. You can find more info about this feature here:
http://www.mp3tag.de/en/help/options_format.html and in Mp3tag's user forums:
http://www.anytag.de/forums/