Nice try, but the problem with house rules is they unbalance the game. Who will buy trannies anymore when you can put infantry on destroyers ? You must then change cost and abilities to the whole shebalong of units, in order to rebalance it, so now you got a brand new game, the A&A Carolina edition. :-D
just for some historical facts, I happen to know about 2 incidents where infantry used destroyers for transport. First was the amphibious assault on Norway 9. april 1940. A German destroyer with a crew of 360 sailors could take 200 infantry as cargo. For the attack on Narvik, 2000 Austrian infantry that was part of an mountain division, did sail on 10 destroyers, from Germany to Narvik in Northern Norway. Their first problem was they could not make an amphibious assault against a well defended shore. They had to debark at a port like passengers from a liner. And the only reason they succeeded debarking at Narvik was the Norwegian officer in command at Narvik was a pro Hitler Nazi. Their other problem was that all heavy equipement and supply had to come on trannies. So there are no way around a tranny. Their last problem was that after 9 days under deck the fighting spirit was low, so they would need a couple of days to recover. There are a reason the Allies made Landing Crafts for the Normandy invasion. Another issue conserning your game is that an average A&A infantry unit is supposed to represent an army of 100 000 men or something, not 2000 men. A rule like this could work in a tactical level game, but now so much in a grand strategy game like A&A. But with that said, this was actually an optional rule in the A&A Revised edition from 2004.
Oh, and the other example I know is the Dunquirk evacuation after the fall of Belgium, this is also in 1940. The myth says it was a fleet of civilian sailboats, rafts and canoes that lifted 350 000 british infantry from the beach over to UK. The fact is, it was 20 british destroyers that did the job.
So to make a house rule that got a link to the real war, I say a destroyer got the ability to ferry, or bridging, one infantry unit across one or two sea zones in the combat phase only, either as amphibious assaulting an empty enemy territory, or if its not empty let the defender roll a preemptive strike, and if the infantry on the destroyer survive, he can attack. Or for a Dunkirk evac, let one defending infantry retreat via a friendly destroyer, even if this last suggestion is blatantly cheesy