Dunno about InDesign as the name suggests, I bat for the other team. In QuarkXPress, there is a setting in the prefs that allows you to specify a default replacement font.
The fact that you are getting this problem at the printing stage suggests that you could have missing fonts.
Are you using PostScript Type 1 versions of the fonts you mentioned? If so, don't forget that you need the screen font (which is activated by Suitcase, or whatever font management software you're using) AND a separate printer font. BOTH must be present in the same folder to work properly.
An orphaned screen font WILL appear to work fine until it's time to print, but if it cannot connect to its proper printer font, it will not work properly. I have yet to come across any pre-flight software that ALSO checks for the presence of the accompanying T1 printer font. Could it be that your system is substituting a default replacement?