No one is saying that code is the science.
If I'm given bad information and I act on that information, then problems can occur.
Similarly, if the software is giving the scientist bad information, problems can occur.
How many more stories do we have to read about some research getting published in a journal only to have to retract it down the road because they had a bug in the software before we start asking if maybe there needs to be more rigor in the software portion of the research as well?
There was a story on HN a while back about a professor who had written software, had come to some conclusions, and even had a Ph.D. student working on research based on that work. Only to find out that a software flaw meant the conclusions weren't useful to anyone and that student ended up wasting years of their life.
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This stuff matters. This isn't a model of reality, it's an exploration of reality. It would be like telling a hiker that terrain doesn't matter. They would, rightfully, disagree with you.