The Tiger convoy passed through, and there were individual merchants that were passed via Malta as well. Fast warships and submarines for transport did not AFAIK go via, but to Malta from either end.
So Axis occupation of Malta would not have changed the convoy routes, as the status quo even with an unoccupied Malta was to not go through the Med. There were substantial mine barriers in the Sicilian Strait, plus of course the risk of air attack from Sicilian bases, and fast warships being based in northern and southern Sicily as well. Who held Malta was irrelevant to the question of Mediterranean passage.
All the best
Andreas