I'm not the op but posted about my own text system. In short, I never used images in my notes even when adding them was easy, so I saved myself the trouble of having to deal with rich document formats. With the goal of portability and tool agnosticism in mind, I believe a plain text file is better for me. Everything can break or be replaced, yet I'll be able to continue my work habits using nothing more than notepad or even EDIT.EXE. I'm reasonably confident markdown or html will be readable for a long time, but I value ultra simplicity here. I think ultimately it's a matter of personal taste.
When I produce images, it's nearly always in the context of a project, which has a wiki or other system. But that's outside of what I'd personally call "notes".
Markdown and html can display local images. The only tricky thing is if you want to place images in separate folders and how you maintain that structure over time.
I believe that charts and diagrams convey a lot of information that cannot be easily reproduced with raw text. I guess it ultimately depends on the topic you are reviewing.
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