really like the idea of developing deep mastery of applications/OS programming.
When you've only just started programming, then you're looking at several years to master it. There's way around this.
Is C++ still worth learning?
You have to start somewhere, and learning C++ is certainly useful.
Would I spend most of my time mastering the MorphOS API instead of learning industry-relevant Linux/Windows APIs? Or is the API issue small fry compared to understanding how C++ works?
Mastery of the language and programming itself are the most important. Once you've taken care of that, using any well documented API isn't a problem.
On the other hand, the thought of spending lots of time learning the MUI API might be a bit de-motivating, knowing it won't be directly benefiting my CV
Of course, but the key is mastering programming itself. Learning how to use an API is part of that.
I don't really see a problem with learning how to program on an AmigaOS related platform, but there are good options for Windows as well, such as Visual Studio (express editions are free, requires a Microsoft account, also free). Because you want relevant skills, just stay away from 680x0 assembly language :lol: