I 'm using this method as the center of my design. (Generated Queries And Custom Queries from XML)

I want to be sure that FillDataTable method is supported with Enterprise server solution.

It is.  100% of the BO logic is supported on the Enterprise Server, that is the beauty of how the ES works.  You can literally change your connection to the ES data source item and your application will then start using the ES instead of the direct connections.