To edit ArcGIS Online hosted feature services directly in ArcGIS Pro, open the catalog pane and click on Portal at the top. You will then see all data you are the owner of under My Content and things shared with you as part of groups My Groups. After that, simply add the layers you need to update to a map, edit as usual (add or edit features, change attribute values, etc.), then save the edits to commit the changes to the hosted feature service that lives on ArcGIS Online.
These changes will all be reflected in your web map without having to re-publish or overwrite a web layer. In practice, it really doesn't work any differently than editing any other feature layer in ArcGIS Pro. The process is much more streamlined than it used to be in ArcMap.
You can also define domains, add fields, or delete fields directly on the hosted feature service in ArcGIS Pro, although some operations on a layer's schema may not be allowed if a layer is actively being used by others or has offline copies in the wild that have been downloaded with Field Maps, etc.