Strictly speaking, EPUB 3.0.1 says this is allowed (or rather, it doesn't say otherwise). However, people (legitimately IMO) asked that EpubCheck reports that as warnings.

Can the spec try to be clearer on which resource it allows being undeclared? e.g. introduce a safe place to put such resources, like in a top-level directory which doesn't contain a Package Document, and disallow undeclared resources in other locations.

See also the thread "validation issue with ancillary resources" in the epub-working-group mailing list, and also w3c/epubcheck#58