SharePoint Designer workflows are not deprecated and will work in feasible future
In Ignite 2016 Microsoft has announced that there will not be SharePoint Designer 2016, but SharePoint 2013 Designer is still supported. It works with SharePoint 2013 / 2016 / Online. SharePoint 2016 and Online is just evolution of SharePoint 2013 version. Nothing is dramatically changed internally. Thus, workflows will be still working in feasible future.
Microsoft has stated on many occasions that workflows will be supported for many years. However, they are not investing a a lot of resources to improve SharePoint 2013 workflows.
SharePoint 2013 workflows proved to be stable and working for long time. I don’t see a lot of stuff to improve especially in SharePoint Online. Our set of Plumsail Workflow Actions extends default workflows with a set of more than a hundred workflow action. Thus, you can still rely on workflows in your business processes automation tasks.
Microsoft Flow provides some alternative, but there are not many actions related to SharePoint. For example permissions actions are not covered at all. Thus, if you want to automate your processes on SharePoint right now, SharePoint Designer workflows + Plumsail Workflow Actions is the best choice.
You can find additional discussion about support of SharePoint Designer workflows on Collab365.