Scrivener needs to make Superscript and Subscript more visible that just showing up in unused icons and it would be really nice if they looked right in eBooks. Since you can do superscripts and subscripts correctly in HTML, I assume that this is a Scrivener problem not an eReader problem.
What are “unused icons”? If you use this kind of formatting frequently, you can add their respective buttons to the application toolbar. There are plenty of optional buttons for lesser used commands available for you to add. Check out the View/Customize Toolbar… menu command.
More precisely it’s an issue general to RTF->HTML conversion, which is handled by the Mac. In general it’s better to use a semantic output system like Markdown if you need clean results. Word processing style environments produce notoriously “dirty” HTML/CSS (though what we do have with the Mac is better than Word at least!) and that’s all we have available for easy conversation at this time. For those that are happy with basic WYSIWYG-ish output, it’s fine though.
You should have some better options in the future though, I speak mainly for the present, above.