The ship only hit the grounds on the sides where it's less deep, but the cables probably go through the middle area where it's the deepest. So there wasn't much of a chance for the ship to damage any cables.
There is no reason to run a submarine cable through a canal, because there is land adjacent to the canal.
There's land adjacent to many of these cables. It is cheaper to bury cables in water -- there's a lot fewer shovels needed and fewer property disputes.
Also cables laid underwater are better protected from theft and vandalism than those on land in possibly hostile territories.
Man-made canals are constantly dredged.
The Suez telecom connections run overland.
It makes little sense to lay cables in the water in the canal, since they're always doing construction, digging, and dredging in and around it.