On the one hand, it provided a base of operations against Axis convoys bound for Libya and forced a significant diversion of German and Italian resources meant to suppress it. It also denied the Axis a potential propaganda win of conquering yet another Allied holding.
OTOH, Malta's exposed location also worked against it - the large naval base built there during the interwar period was abandoned by Cunningham's ships before the Italians had even fired their first shot, due to the threat of air attack, and relocated to the much less developed Alexandria. This isolation also meant that the British expended a significant amount of resources in their efforts to hold and resupply the place - numerous ships (including carriers!!), hundreds of aircraft etc - resources that could have maybe been used elsewhere to greater effect.
Also of note - Rommel's supply bottleneck was always port capacity and distance from the ports to his front line, not losing ships on their way to Tripoli or wherever.
So, thoughts?