Is the amount paid for the loan used to build the commercial shop subject to Zakat, or is it considered an expense?

There is no obligation to pay Zakat on the amount paid to settle a debt. Zakat is only due on wealth that is present at the time it becomes obligatory. We should note that the agent in a Mudarabah (profit-sharing partnership) does not own their share of the profit until after distribution and separation, because any loss in the Mudarabah capital is compensated from the profit if it occurs.