Via Routes

I am planning expand my network from South East Asia to US territories. My Question:

CGK to JFK via HND. These means I will have only bookings for CGK - JFK  Routes BUT no Bookings for CGK - HND, HND JFK and vv.? 

You have bookings for CGK-HND and for CGK-JFK (and the return routes). But you do not have booking rights for HND-JFK. This is assuming, you're home market is in Indonesia.

What if that flight is packed with CGK-HND passengers to the exclusion of CGK-JFK (more valuable) passengers?

That’s bad luck then. You’ll have to try it.

Another way of seeing it (equivalent to matth's):

What if that flight is packed with CGK-HND passengers to the exclusion of CGK-JFK (more valuable) passengers?

Then you should run one or more CGK-HND flights and check whether a separate, nonstop CGK-JFK would also fill up

I did make direct flights not VIA for now lets see if the routes are feasible else, i have to rely on Interlining Agreements :)

good luck!