The issue is exposed by the tck tests: SQLPathTest#testChildAxisRoot

The test scenario involves using a readonly session and executing the following query: SELECT * FROM nt:base WHERE jcr:path LIKE '/%' AND NOT jcr:path LIKE '/%/%'. The results are asserted against session.getRootNode.getNodes().

The result is that only "/" (mode:root) is found, instead of /testroot and /jcr:system. Using a directory to store the indexes and looking with Luke at the indexed content, it does appear as if the above mentioned paths aren't stored in any document.