Most academic code is written fairly naively (it's usually the code that's written by people who have some idea and try to be "smart" that's a problem), and so can be cleaned up and made maintainable pretty easily. If AI causes more "smart" code to be written, that's going to make things worse.

On old hardware/software, that's normal, and will continue to be normal, simply because the value is in the instrument, and money spent trying to get the software/drivers to work on more modern systems would be better spent on buying a new and better instrument. The only way this would change is if we force all hardware vendors to fully open-source (and ideally upstream) their code (look at the whole IoT ecosystem).