I created some EPUBs with small caps a while ago using sigil, and the code there looked like:
Code:
<small>I SEEM TO BE</small>
So, it looks like the same font is used for small caps and the standard text. It just has the <small> tags around the small caps. There are no issues with the font being tiny that way. I don't see how to automatically change your EPUB to follow that style, though.