I don't use a Simulink model, but instead rely on extensively commenting my code, writing documentation for main functions, as well as sub-functions, and try to keep the names of my variable clear, concise and meaningful. To this date that has been enough.
Switching to Simulink has major drawback: you need additional licenses, so you reduce the number of people who can use your code and the number of people who might help you solve issues.
For me personally, using sub-functions and comments is enough to follow the program flow, even for older projects I haven't touched in a while.
(Because 'just try harder'/'do it my way, you silly' is not very helpful most of the time (or plain arrogant), I chose to add my thoughts as a comment, instead of an answer.)
