Yes, Aldiko must extract the cover. At least, on my Android phone, if I put an .epub in the /ebooks/import folder for Aldiko, set Aldiko to import books, the book is imported into Aldiko.
It creates an ebooks/author/book/ directory, places the .epub in there and creates a .cover.png and a .thumbcover.png for it automatically (as well as a .nomedia file)
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