Ok, I tried this. I used Sigil to make a simple ePub, and put in an href of
http://maps.google.com/ to the words "map here". Then I loaded it into Stanza.
If you select "maps here" (not easy, because Stanza tends to read presses as either page turns or access preferences), it will load the external link....but in an internal Stanza modified webkit browser, not Safari. (other iPhone apps do this as well-including RSS readers and Twitter clients). There is a "Safari" button to load it into Safari, but..uh..it added some odd text to the link, so not sure what is going on there.
I'm guessing a map location would work as well, but it does NOT open the Maps app, just the google maps page in a webkit browser still within Stanza.
Edit: Ok, I tried using the Google Maps coordinates link for The White House...it again opened google maps in the Stanza browser thing, and correctly loaded the satellite view of the White House. The title bar of the window was the Link name: The White House.
The Safari button still does not load it into Mobile Safari. Using the same link IN mobile Safari gives me the option to "Open in Google Maps" app, which is probably what you want it to do in the first place.