The domain is complex, the customers require a high level of correctness, and features are often implemented to try things out in the lab and then abandoned once it's a dead-end in the real world. Oh, and most academics don't have money to pay for software, nor do they respect the software engineering process.
Commercial gui-based software is usually sold along with proprietary equipment like a microscope or something, and universally loathed even by people who managed to wrap their heads around it. It's much easier to work with different software from different people or groups if it's all the same syntax, rather than relearning clunky proprietary gui after clunky proprietary gui.