Unix assumes any file without an extension is an executable file. the Classic (pre OS X) Mac OS did not use extensions/suffixes, but depended on internal Creator and Type codes to identify the application associated with a particular file. Unix (including OS X) does not recognize these codes, and requires an extension.
For AppleWorks, the extension is .cwk.
Add that extension to your AW5 filenames and they should open in AW6.
As for the dropping of the Superdrive, this seems to be just the most recent step in pushing the Mac into the present. The first second was dropping the 3 1/2" floppy drive from the original iMac. Prior to that, the first Mac had a 3 1/2 inch floppy, but not the 5 1/4 inch version used earlier on the Apple ][ series. Have you had need to use a floppy recently?