Despite the near impossibility of extracting embedded fonts from PDFs, some type foundries still prevent their fonts from being embedded in PDFs. While that choice is certainly the type designer’s to make, it can create quite an annoyance for an Illustrator user.
When you save an Illustrator CS/CS2/CS3 document using the default options, Illustrator automatically creates a PDF compatibility layer in the AI. That PDF layer enables the AI to be opened in Acrobat or Adobe Reader (among other functions). It’s a big convenience. However, when you allow Illustrator to add that PDF compatibility layer, it also tries to embed the fonts you’ve used. If you use a font whose creator has disallowed embedding, Illustrator will warn you that the particular font can’t be embedded.
And it will warn you again every time you press CMD+S/CTRL+S to save the file, which, if you’re smart, you do every few minutes. What a pain!
The easy way to stop that warning from appearing is to save (or resave with the File > Save As command) your document without a PDF compatibility layer. Begin saving or resaving the file as normal. When the Illutrator Options dialog appears, uncheck the Create PDF Compatible File option in the middle of the dialog. You’ll notice that doing that disables the Fonts section above it. Click OK, and your document will be saved without fonts embedded.
The drawbacks to this trick is that, if you want to send the AI to someone else for editing in Illustrator or even just viewing in Acrobat or Reader, you’ll have to send the fonts as well separately (a probable license violation). They won’t be embedded in the file, so the recipient will have to install the fonts you send.
Of course, if you don’t send out your AI files, this won’t be a problem.