We're probably looking at iOS 12 before the Workflow acquisition starts to bear any native fruit...
Apple won't have acquired the app without having a plan for it or its developers, and some form of native automation seems almost inevitable, although most likely in the context of Siri and AI rather than in Workflow's current remit.
A year ago I was worried that once we had some form of native automation, that would likely be limited in comparison to the Workflow app, then Workflow would be removed from the App Store leaving a void. I'm not so worried anymore.
Siri Shortcuts and Workflow look similar and both serve to make regular, repeatable actions easier to perform but they are complementary rather than fighting for the same territory. Shortcuts looks like it will let you string together a number of discrete actions into a sequence whereas Workflow operates on the intra-app level allowing you to connect them to achieve an outcome.
Shortcuts seems to be more a case of do A, do B, do C while Workflow is most powerful when you go from A, through B, to C. It's a different use case and, because of that and even if they iterate and overlap, I think Workflow is safe.