This is a tricky field.
ADE requires true small caps and does not recognize emulated small caps.
The usual (MS) fonts lack a true small cap font though. So, if you want to add true small caps, you should consider using embedded fonts. But some e-readers don't recognize embedded fonts. A catch 22 problem...
If your headers have small caps, they should be recognized as such but you must give them in the CSS stylesheet not only a font-variant:small-caps
but mainly a font-family
with small-caps support. The span element is required only for text within a paragraph.
Now that I have been pretty unclear, I let you consider one EPUB like the joint one. It makes use of embedded fonts, small-caps for titles and part of text. Could be an example of what I meant to say.
I cooked this EPUB with writer2xhtml (short is W2X) and Sigil.