I can confirm (through my own empirical observation, only: I do not see this addressed in the official docs) that writing a log entry is faster than writing a storage entry. Thinking about it, that makes sense: log entries are always appended, no indices, no particular transactional issues (beyond atomicity of each log-entry writing), etc etc; being so strictly limited it makes sense that they can be more optimized.
However I once (very very early on in the pre-beta days over a year ago) observed one case where I thought there should be a log entry I had written but just couldn't find it; I was unable to reproduce the observation, it may have been a glitch in my code or a since-fixed bug in GAE, but it makes me wonder a tiny bit about data integrity -- how guaranteed is the logs' integrity? Until and unless I see something in the docs explicitly about it, I'm not going to feel I can count on the logs for 100% integrity -- if accidentally losing one record in a million would be an absolute tragedy, maybe going for the store's higher guarantees is worth the performance impact.