Yes, you can use Bayesian Networks to run “what-if” scenarios provided your network can be interpreted causally. This means that nodes are not just linked because they seem to be related observationally, but because there’s a cause-effect connection between them.
For an introduction to Causal Inference (the discipline of discerning observational from causal relationships) you can read Judea Pearl’s: “The Book of Why: The New Science of Cause and Effect”. Incidentally Judea Pearl was the one who coined the term “Bayesian Networks” and devotes a chapter of the book to discussing them.