I figured it out.
When you first add an MPC Controller to your simulink model, it has one measured disturbance input by default. From the Block Parameters window (after double-clicking it) you need to uncheck the box next to Measured Disturbance (md) in the Additional Inports area and click Apply, before cliking the 'Design' button:
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Then when you click Change I/O Sizes in the designer there is no field for Number of measured disturbances:
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