Hello,
you can't completely exclude / turn off indexing and expect all searches to work just the same. The transactional metadata query does just what it says - it queries metadata, not everything that the indexing search subsystem supported. It has restrictions (look at the documentation in docs.alfresco.com) in what query elements it supports, i.e. even if you are "just" querying metadata, there are some metadata query constructs that it does not support (i.e. OR queries, wildcard / case insensitive text matches).
Regards
Axel