No it's not, it depends mostly on the tone of the voice. It's often enough sarcastic, but really doesn't have to be.

Just like data consistency doesn’t exist in MongoDB

Then you have to follow the principle of charity and assume they're being nice.

I think it sits on the same level as ' it's interesting',when 9/10 times you could see that the person who said so is not even remotely interested.

I'm not sure I agree with that. A lot of the time "interesting" serves as a filler word for "I'm not totally sure what to think about it" or "I'm not ready to articulate in 1000 words why X may or may not be a good approach right now."

"That's nice" is a way of explicitly stating that you don't care to any degree about whatever the other person just said.

It's very context sensitive. "That's nice" (with at least an implied exclamation point) can be a literal reaction to something you like. "Yeah, that's nice" as a reaction to a statement/argument can also be the equivalent of "Whatever." i.e. it's stupid but I'm not even going to dignify it with an explanation of why it's stupid.

What if it really is actually nice?

"How nice!" is a positive exclamation with minimal wording change from "that's nice".

You can also be explicit about who's being nice. "That's nice of you."

This really depends on what you want to mean by "nice".

Then you have to struggle to find another word to say that it's nice, remembering that saying "it's interesting" is forbidden, too.

I use Great so consistently sarcastic that my kids have unfortunately learned that Great means something not great.