This is something we will be looking at in detail early this year. High-load multi-user performance testing is high on the priority list.
I would expect the performance of the JCR API to be a little lower than the pure Alfresco APIs as they are another layer mapped on-top of the Alfresco APIs. However, it shouldn't preclude you from using them as it won't be significant! Lucene performance has proven to be good so far, it is our aim to make sure you can search a repo of millions of documents in sensible response times.
Thanks,
Kevin