I'm a PhD student in Electrical Engineering. I'm currently working on a Monte Carlo-type simulation for looking at the underwater light field for underwater optical communication (no sharks!). I'm doing the development in MATLAB and I recently put all my code up on Github (
https://github.com/gallamine/Photonator) to help avoid some of these problems (lack of transparency). Even if nobody ever looks/uses the code, I know every time I do a commit there's a change someone MIGHT and I think it helps me write better code.
The problem with doing science via models/simulation is that there just isn't a good way of knowing when it's "right" (well, at least in a lot of cases), so testing and verification are imperative. I can't tell you how many times I've laid awake at night wondering if my code has a bug in it that I can't find and will taint my research results.
I suspect another big problem is that one student writes the code, graduates, then leaves it to future students, or worse, their professor, to figure out what they wrote. Passing on the knowledge takes a heck of a lot of time, especially when you're pressed to graduate and get a paycheck).
There's got to be a market in this somewhere. Even if it was just a volunteer service of "real" programmers who would help scientists out. I spent weeks trying to get my code running on AWS, which probably would have taken a few hours from someone who knew what they were doing. I also suspect that someone with practice could make my simulations run at twice the speed, which really adds up when you're doing hundreds of them and they take hours each.