It's more that it closes the overland route through the now-Suez canal. There was still a way to discharge things, and even if not for massive amount of goods, it still really helped for communication.
Closing Egypt forced them to use the Cape of Good Hope route, which significantly slows communication.
Also, he was hoping to (and did) find the Pharaoh's canal to go from the Med to the Red Sea. It's important to see Mysore was still around and could have provided a counter weight to the British and a beach head. French India had been massive not so long ago by then