The least techie way involves having the Quality Check plugin installed. You can use it's epub search to search for 'version=3.0' or 'properties="nav"' in the OPF file. See the attached image for how I set the search. For my Intake library, this reports 37 ePub3 files out of 58 total epubs.
Otherwise, you can open it in Sigil or the calibre e-book editor and take a look at the package version in the .opf file.You can also tell by multiple other tells such as seeing properties="nav" attached to one of the xhtml files.
Code:
<package version="3.0" unique-identifier="BookId" xmlns="http://www.idpf.org/2007/opf">
Code:
<item id="nav.xhtml" href="Text/nav.xhtml" media-type="application/xhtml+xml" properties="nav"/>