Ships that were sunk by the Egyptians in late 1956 during the Suez Crisis blocked the canal for several months. It's one thing to sink a ship by boarding it and scuttling it, quite another to sink moving ships by planes during WWII. As we discussed recently with the possibility of a Pearl Harbour type attack on Scapa Flow, Germany had very few long-range naval bombers. I don't believe they had the capability to fly all the way across the Med, and hit enough ships to block the canal, in a surprise attack. If you look at the picture I posted earlier you can see the (tiny) white wake of a ship entering the canal. If you sunk that it wouldn't block the canal. You would have to hit several ships or catch one in a narrow section of the canal. There were less than 50 ships passing through each day, so it's not like you would have lots of targets.
You would surely have more chance of causing problems by dropping mines into the canal. But that requires low flying, and it was defended with AA and fighters based in Egypt. Or a St.Nazaire type raid, where an old destroyer loaded with high explosives was sailed directly into the port and blown up.