What should be the Jenkins pipeline strategy for deploying multiple cloudformation stacks in a repository via Jenkins?
There are a ton of different ways to do this; and the unfortunate answer is "do what works for you"; particularly with regard to your pipeline and branching strategy.
You can either create a single pipeline for each stack, or one pipeline to deploy everything. If you go with the one pipeline to deploy everything, an important part of CloudFormation is that, if a template hasn't changed, CloudFormation won't do anything. Therefore, if a commit only updates one stack out of X that you are deploying, only that one stack should update in AWS as there will be some comparison between the templates you're submitting for the update and how they exist in AWS and decide whether or not to update based on any differences.