If you set those restrictions on the queried entities you are definitely right, the quried entities should be filtered accordingly and not the relations.
But if i filter the relations i actually want them to be filtered (for good reasons). Fetching the relations afterwards is not an acceptable solution as it triggers extra queries. Please take a look at my forum post describing a "real life" problem:
This fix currently prevents us from updating to hibernate 3.6.4 or any newer version.