After a ton of research, I decided to do a lot of keys only queries in my code. Part of the reason being the following quote from Google's App Engine Pricing Page (yeah, it's amazing when coding means money).
Calls to the datastore API result in the following billable operations. Small datastore operations include calls to allocate datastore ids or keys-only queries. These operations are free. This table shows how calls map to datastore operations:
So for the past few months, I have taking a free ride. This morning, with very little activity on my website, my Datastore Small Operations has reached its quota and is now red, causing trouble on my website. Does anyone here knows if someone has changed on how Google bills Datastore Small Operations? Has the API changed somehow causing my existing code to be considered poor engineering design? Thanks for any insight on this issue.
There is no limit on the number of small operations if you have billing enabled. Without it, the limit is only 50,000 operations.
Since these operations are free, it would not hurt to enable billing.