Best Practices to create DataFlow from Sharepoint Folder

If there is a connector called Folder or SharePoint Folder available in Dataflows Gen2, then I would use that connector and paste the SharePoint Site URL in that connector.

Then I think you should be able to browse the folder contents and load folder items into the Dataflow Gen2.

I think the number of Dataflows depends on your preference. 

I haven't thought about this specifically for Dataflows Gen2, however for the Power BI dataflows, I think the number of dataflows is a trade-off between easy to administer (favours creating one or few dataflows) and on the other side reducing the possibility that failure in one query prevents other data sources from being refreshed (favours creating many independent dataflows, e.g. creating one dataflow per query).

Also, editing a dataflow can be slow if there is a lot of data in the dataflow. Which might favour creating independent dataflows.

Access control might also be an aspect. If you need to give different access permissions for each dataflow, then I think you need to place the dataflows in separate workspaces. At least for Power BI dataflows this is true. I haven't studied it for Dataflows Gen2.

Ultimately, I think the answer is "it depends" and use a balanced approach.