Workaround: One can use the $smwgNamespace setting in LocalSettings to provide the correct base URI manually. See http://semantic-mediawiki.org/wiki/Help:Configuration#smwgNamespace.

Thinking about this problem again, I note that it is not a bug but expected behavior that can easily be customized: The main purpose of URIs is to provide unique identifiers for wiki pages. This is why they should not depend on the way in which the wiki is called. However, the port number can only be determined automatically based on the current request. So if the wiki was reachable via multiple ports, then the URIs would be different depending on how the wiki is accessed.

In order to solve this problem, SMW does not automatically generate the base URI but rather lets the user set it explicitly: it is the single parameter given to "enableSemantics()" in LocalSettings.php. In order to get port numbers in URIs, it is enough to add the port number to this parameter.