I took a set of ten or fifteen epubs that I have, all non-DRMed, and dropped them onto iTunes. It imported them without error messages. I have no way to test if they're actually OK because I don't (yet) have an iPad to sync them to. But anyway, to continue.
Two of them have cover art in iTunes. The rest do not. Huh?
If I look at them in Calibre, they all have cover art. Furthermore, something odd - if I go back into iTunes and look at one of the ones whose cover art shows up in the 'Summary' section of Get Info and in the cover view, although the cover shows up in the 'Summary' section there's nothing in the 'Album Artwork' section. I cannot copy or paste the cover in the 'Summary' section (they're greyed out, and I tried).
Going back to the ePubs as it was saved to disk by calibre, I can compare a working ePub and a non-working ePub. They both have cover art in their folders, and both are jpgs. Opening them in preview shows both of them are identically sized; both are using the same (RGB) colorspace. They look identical. But one of them imports when you drop the folder of the ePub on iTunes, and one does not.
If I paste the cover art into the non-working ePub's 'Album Artwork' pane in iTunes, it shows up as having a cover, and that cover shows up in the Album Artwork pane. The one which worked originally still doesn't have anything there.
So if I had to hazard a guess, I'd say there is still something screwy with iTunes' ePub import function; something which screws up some cover art. Great. I don't want to have to go manually re-fix all my cover art on my 200+ books.