I don't know about Adobe Illustrator, but I know that in Inkscape, it's best to save the SVG as "Plain SVG" rather than "Inkscape SVG" if I want the file to work (well) with other applications.
But what program are you using to check to see if the SVGs are showing in the ePubs? Adobe Digital Editions? Have you checked the (x)html files that call the SVGs inside the ePub in Firefox or just the SVGs? Have you tried any other browsers?
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