Inglorious Rasters
Embedded files do not show their origin in the document info palette - linked files do. However, once rasterized, the file link disappears, and that's the problem you're up against.
There's nothing innately wrong with embedding an image in an Illustrator file - no different than inserting an image in a PDF file really. And if it was verboten, as someone above has suggested, then why does the program give you a choice?
I know lots of designers, myself included, who use Illustrator to create web artwork, which of course needs to be rasterized before using it somewhere else. I would usually keep my artwork in vector format and simply "save for web" to create a bitmap version and keep my nice vector file for editing, but sometimes a quick raster is all I need...
Linking images to an Illustrator file is NOT the best practice for making self-contained files, especially if you intend to further embed your Illustrator EPS in another document. There are no hard-and-fast rules about this - it depends on your "workflow", i.e what came before, and what will come after your Illustrator work.
You do whatever best suits your workflow with the tools at hand, and Illustrator is a big bag of tools - so don't limit yourself artificially based on what "someone told me". Manuals are, contrary to popular belief, just full of information about these exact issues.
Cheers,
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