Hi
Under the hood, the CMIS query implementation currently has two versions - STRICT - which complies exactly with the spec and NOT_STRICT which has minor violations you would not notice (and mostly like) and aspect only JOIN - which does not require a real join. See the wiki page. The STRICT version does not support JOIN; the NON_STRICT supports join for aspects.
I believe STRICT was the default and has now changed.
You will have to use the search service or update to 3.4.
There is no way to select the version exposed over the CMIS API as part of the request, or turn on join.
It was pointed out to me recently that query is itself an optional part of the spec.
Andy