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This only issue with margin-top being ignored that I'm aware of is the margin-top assigned to the first element following a "soft" page break--achieved using the page-break-(before|after) css attribute. That's mainly because the wording of the epub2 spec implies that honoring it in that situation is not required. Everybody's learned to deal with or work around that one.
I've personally never really run into too many devices/apps that had trouble with honoring the margin-top -bottom attributes outside of that situation.
Margin-top -bottom is the preferred method of creating differing amounts of spacing between various sections in an epub document, after all. It's easy to quickly adjust in one or two places in the stylesheet instead of having to search for empty paragraphs sprinkled throughout the document and add/remove them later to change the spacing. *shrugs*
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