Qlik Sense Desktop is a data discovery tool or I can say It has fully functionality of Qlik Sense HUB but Its is quite personal or made for individual , You can have data security or governance with it so without these two factor BI is in complete. Please develop you client application on Hub from first day so it will ave your time later.
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You can develop your apps in either Qlik Sense or Qlik Sense Desktop. There is no difference except, you have to import your app into Qlik Sense if it was created in Desktop. The connections will be imported as well, with one nuance: if there is already a connection in Qlik Sense with the same exact name that exists in the app you're importing, the connection is not imported.