For Malta, I assume the unit inside consumes 4 supplies, hence the 96 left out of 100. The 9 you mentioned is, I believe, the supply level of the hex. Supply sources, ports with supply stockpiles and hexes connected by rail to one of those are always the highest supply level (9) therefore allow for max recovery to units there. A unit in supply level 6 hex, for example, would get about 2/3 of the recovery of the same unit in a supply level 9 hex. And yes, supply convoy are automatic.
Hope it helps (at least for Malta).