You're right that more resonance structures usually means more stable, but that is a generalization and you sometimes have to look at things more closely. In the case of the ester enolate some of those resonance structures transfer electron density back to carbon, destabilizing the enolate. Draw them out and you'll see.
As for ketone vs. aldehyde acidity: for a simple case consider the electron donating ability of a hydrogen vs. an alkyl group.