At that time on Chrome we were just figuring out a process to remove features and were pretty conservative. We debated a lot about the right way to remove things without causing damage to the web ecosystem. In an early attempt we had failed trying to remove a legacy feature and needed to revert it. It had broken a big company who had then contacted Google directly about the business impact and it taught us a lesson about being careful.
IIRC WebSQL had very high usage and we didn't seriously considering removing it. It's also pretty self contained so the cost on the engine isn't that high.
Chrome still supports WebSQL today because the usage remains quite high at 1%: https://chromestatus.com/metrics/feature/popularity#V8SQLTra...