Using connections is much more efficient (generally) than using queries. With queries, it is the number of search terms that can be a problem, not the number of entities in the collection. Large collection sizes shouldn't really impact performance. Please share an example query if you can - maybe we can help optimize?
Also, we are just putting the finishing touches on a major upgrade that will significantly improve performance of the API BaaS product. Ask your contact at Apigee for more info.
One last thing to consider is that our developer offering may not have the same performance as our paid products. Apigee strives to offer awesome performance on developer, but because of the architecture and SLAs of our paid offering, we can definitely cater to your needs to make sure you have the performance required.