It can be cristals and photons. Carbon is the basis of life because it's good for looooong molecules. But it's not like it's the only option. It may not even be the best option on planets with different temperatures or pressures.

Anyway life may not even need food or care about the passage of time.

I'm not an author, I'm a scientist. So I don't know what the through process of authors are. But I it probably would take long time to actually find alternative ways to do the things same as us but underwater. The civilization won't be like us, they would not have same technology, they wouldn't have same values. Authors are probably trying to capture general population's interests by making things they understand.

And do you think "hey I haven't heard anyone say something to me about earth rotating sun" would have been a good counter argument in the past.

Water is incredible, we don't know all the ways we can use it. Sometimes it takes hours to simulate what water does in seconds. Unlike other materials like metals, which are lot easier to predict. And if we're talking about aliens, don't even have to think water, it could be something else as flexible as water, while having properties that makes it easier to use.