The function defaultSearchBackend() in PrefixSearch.php is supporting only one namespace among all the namespaces specified for the search.
This behavior has been corrected but the fix has been reverted in 2014.
According to ebernhardson, it « looks like the single namespace restriction was put in place in 2008 [...] at the time it looks like the custom lucene search engine that was being used couldn't support it ».
This problem is notably affecting the autocomplete search functionnality.