@daanikus through our company we filed a support issue with GitHub that I hope we get a response to soon. In summary I can confirm the behavior that you are seeing and can also provide repro steps.
The issue is that the check run/suite pull request property is only populated with values on the very initial Pull Request creation step. If you do any other commits to that branch, after the PR was created, the check run/suite events pull_requests property will be empty for each of commit shas’ check runs/suites. You can confirm this pretty easily by taking a close look at the events submitted to your web hook/github app, and it definitely seems like a bug on their side. We are using GitHub Enterprise 2.16.4 here and based on their change log from 2.16 -> 2.18, it doesn’t seem they have specifically addressed this issue or just haven’t documented it.