When using modeling tools like system dynamics, it's useful to keep in mind George Box's quote that "All models are wrong, but some are useful".
When using a modeling tool to describe any form of social system you're creating an imperfect copy of it. This imperfect copy embeds what the modeler (rightly or wrongly) views to be important and how they believe the system to work.
The resulting model, though always wrong to some extent, may be useful. It may help you obtain a better understanding of a system and cause positive change in an organization. On the other hand it may not be useful, it may even mislead you.
You can think of modeling a lot like various software engineering practices like Agile. Sometimes these help teams, sometimes they don't. At the end of the day though, it's really about the teams using them not the specific techniques.