These incentives exist but are not a good excuse in my view. I'd recommend reading this blog post about how "incentives" are used to justify all sorts of bad behavior in academia:
http://www.talyarkoni.org/blog/2018/10/02/no-its-not-the-inc...Right now I'm nearly done a PhD in mechanical engineering. I've worked on several computational projects of varying levels of code quality from good (e.g., NIST's Fire Dynamics Simulator: https://github.com/firemodels/fds) to bad (won't give unambiguous examples for obvious reasons...).
I see clear incentives against uncertainty quantification and high quality model validation in my field. Those topics are treated superficially if at all, because people just want their model to look good, and if they do a rigorous job, that increases the chance that their model looks bad. As far as I'm concerned, if you don't do good quality model validation, you're not doing your job as a scientist.
A more specific example: Some codes are kept for a decade or longer if the software is sufficiently complex. One code I worked with was used by multiple graduate students over several PhDs and had very little if anything in terms of documentation. What did exist was far out of date. I spent a fair amount of time trying to understand and document the software, but other people treated me as if I was crazy for wanting to understand the black box I was provided. I don't think I ever actually understood that software fully despite the many hours I spent working on it. And I'm not certain that it provided correct results either. There were almost no tests, and the existing tests were hard to run and were consequently almost never run. The software produced several PhDs, though. The first few PhDs had it fairly easy. I had to pay their technical debt, and I couldn't pay it all back. It made me look bad as far as I'm concerned and did not save time in the long run. If anything, there's a long term incentive toward good software development practices.
Ultimately I think the solution would involve having minimum standard for scientific software quality, or else grant funding will be withdrawn. It will anger many people who have so far gotten away with writing low quality software, but beyond that I don't see many downsides.