(Disclaimer: my background is in materials physics, and it may be different in other fields. But I doubt it.)Unfortunately there is very little direct incentive for research scientists to write or publish clean, readable code:
- There are no direct rewards, in the tenure process or otherwise, for publishing code and having it used by other scientists. Occasionally code which is widely used will add a little to the prestige of an already-eminent scientist, but even then it rarely matters much.
- Time spent on anything other than direct research or publication is seen as wasted time, and actively selected against. Especially for young scientists trying to make tenure, also the group most likely to write good code. Many departments actually discourage time spent on teaching, and they're paid to do that. Why would they maintain a codebase?
- Most scientific code is written in response to specific problems, usually a body of data or a particular system to be simulated. Because of this, code is often written to the specific problem with little regard for generality, and only rarely re-used. (This leads to lots of wheel re-invention, but it's still done this way.) If you aren't going to re-use your code, why would others?
- If by some miracle a researcher produces code which is high-quality and general enough to be used by others, the competitive atmosphere may cause them to want to keep it to themselves. Not as bad a problem in some fields, but I hear biology can be especially bad here.
- Most importantly, the software is not the goal. The goal is a better understanding of some natural phenomenon, and a publication. (Or in reverse order...) Why spend more time than absolutely necessary on a single part of the process, especially one that's not in your expertise? And why spend 3x-5x the cost of a research student or postdoc to hire a software developer at competitive rates?
I went to grad school in materials science at an R1 institution which was always ranked at 2 or 3 in my field. I wrote a lot of code, mostly image-processing routines for analyzing microscope images. Despite it being essential to understanding my data, the software component of my work was always regarded by my advisor and peers as the least important, most annoying part of the process. Time spent on writing code was seen as wasted, or at best a necessary evil. And it would never be published, so why spend even more time to "make it pretty"?
I'm honestly not sure what could be done to improve this. Journals could require that code be submitted with the paper, but I really doubt they'd be motivated to directly enforce any standards, and I have no faith in scientists being embarrassed by bad code. Anything not in the paper itself is usually of secondary importance. (Seriously, if you can, check out how bad the "Supplementary Information" on some papers is.) But even making bad code available could help... I guess. And institutions could try to more directly reward time put into publishing good code, but without the journals on board it may be seen as just another form of "outreach"--i.e., time you should have been in lab.
I did publish some code, and exactly two people have contacted me about it. That does make me happy. But many, many more people have contacted me to ask about how I solved some problem in lab, or what I'm working on now that they could connect with. (And are always disappointed when I tell them I left the field, and now work in high-performance computing.) Based on the feedback of my peers... well, on what do you think I should've spent my time?