The noquery type attribute should take place on a node-by-node basis, not on an entire hierarchy of nodes. In other words if a parent node is not queryable but its children are, they should still turn up in queries.
Taking a look at, for example the reindex() method, it just returns when it finds a node which is not queryable, ignoring all the nodes below it.
If you're referring to modeshape/RepositoryQueryManager.java at master · ModeShape/modeshape · GitHub, that is something else, not the check for the noquery type attribute.
Should that not continue to check all the child nodes, which may be queryable?
Again, if you're referring to the line of code from above, the answer is *no*. The cache.isQueryable method refers to an internal(system) attribute which is used for branches of the system area which will be skipped from indexing altogether - for example versionable nodes.
That *has nothing to do* with the noquery type attribute.
Ah, alright. I will test further with the noquery nodetype and see if it the problem I'm seeing occurs on the 4.2.0.Final release as it does on the 4.3-SNAPSHOT.