Well, all *.xql files below www are loaded, and it is possible to put the named queries for subsites into, say, index.xql in /www. I just checked it. However I find this solution a bit messy. IMHO it is more elegant to keep all files belonging to a particular subsite in a single directory, specified through the subsite parameter.
I will add an explanatory comment to the bug report, and let the powers that be decide what, if anything, should be done about it.
