Most carrier-based multi-purpose aircraft (ie: fighter/bombers) today are jets with single or twin jet engines that pack way more thrust than a bunch of WWII-era propeller engines. So of course they can pack a larger bomb load on a much smaller aircraft. All aspects of aircraft technology have come a long way in the last 67+ years.
But the carrier-based bombers and torpedo planes of the 1940's were rather light on the bombload, and were never used for extensive city bombardment like the multi-engine land based bombers were. While they did participate in bombing specific military targets like individual ammo dumps, warehouses, docked ships and the like during fleet raids on coastal Japan and Formosa late in the war, their primary targets were usually enemy naval ships and amphibious landing air support. They were incapable of strategic carpet bombing or knocking out cities.
In the one instance where a larger twin-engine B-25 Mitchell bomber (and not a 4-engine bomber as depicted in CiV) was used off of the USS Hornet during the famous Doolittle raid on Japan, they literally had to strip everything but the airframe and the aluminum skin out of the planes to make them light enough to make the short takeoff from the deck, and they could never have landed on it again. It was truly a freak situation, never repeated during the war.
Regardless of these facts, I have no issue with them allowing a 4-engine bomber to use carriers in CiV, as it would have required a new and different unit to accurately depict the form and capabilities of the real carrier-based bombers of that era, and there really isn't any need- the game isn't 100% historically accurate, and was never intended to be. But by the same token, I also see no need to allow stealth bombers to be carrier-based, either. By the time you have stealth bombers, you already have nukes, and can launch them from carriers, subs, and cruisers if you really need long range sea-borne mass destruction. Redundancy.
And if you really must have carrier bombers late game, just save some of your WWII era bombers and don't convert them all to Stealth bombers. Problem resolved.