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HTML entities are like putting ᾚ in the source wherever you want "Greek Capital Letter Eta with Psili and Varia and Proscegrammeni", which will display this: ᾚ if you've a proper supporting font on your system.
One possibility is that your embedded font may not be Unicode, and whatever mapping it uses doesn't match the encoding of your source page.
Another is that ADE/Sigil code view/whatever, works better with precomposed characters in which the diacritics were designed to be part of the character, rather than the software having to take an existing character and then applying the appropriate diacritics to it. I know there are some other text editing/viewing apps that choke on having to do that.
Perhaps if you could hunt up the entity equivalents for the precomposed versions of the characters you'd like to use, you might have more luck displaying them.
And of course there's always just ADE being buggy and not supporting useful stuff, which is what I'd personally lay money upon.
Speaking as a reader, I'd rather not see text excluded if it's reasonably relevant and possible to put it in in some way. An image is not the optimum solution, but better than nothing, imho. You never know when someone will actually be able to read ancient Greek*. It's too bad there's no inversion of the <object> tag, where you could have text with an image fallback instead of the reverse.
Maybe you might like to try faking it by putting in the text with a link to the image, and a note in the front of the book saying "The original text of this book included footnotes in a language that your e-reader may not display properly. If you find that these footnotes are not appearing to you, please click on them to see an image of the footnote taken from the original text." or words to that effect.
* I'm assuming this is what you need the diacritics for and the more obscure polytonic combinations are giving you trouble, because if ADE truly doesn't support the rather simple few that monotonic modern Greek comes with, then that's really pitiful.
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