Projection queries can be much faster than 'entity' queries in Breeze because, in general, there is no need to merge the result of a projection into the EntityManager cache, which is a time consuming process if you have a lot of entities. ( Some caveat's here if the projection itself contains entities).
If you do not need this capability or only want it some of the time Breeze has a 'noTracking' method that you can call on the query. (see: the 'noTracking' section on this page: http://www.breezejs.com/documentation/querying-depth ). No tracking queries, especially those involving a lot of entities will be MUCH faster.
In terms of Debug vs Release performance, this is presumably purely a 'server side' issue and in my experience is largely a Visual Studio artifact.
Note that if most of your work is just client side javascript can have your server run in a separate solution in 'Release' mode, and just start it up once and leave it running. Iterating during the development of the client side is then much faster.