Aside from the specific objections, the real problem (alluded to above often) is that the sheer volume of gas you'd need means that what you'd have would basically be an airship somewhat overburdened--frankly if you
could make the gas cells on a scale sufficient to lift a significant percentage of the ship's weight, you might as well kick it up to 100 percent and have yourself a proper airship, flying around in the sky completely independent of the water!
Water is about 800 times denser than sea-level air. To be sure a surface ship has most of its volume above the water line, which is to say the volume contained in its structure is less dense than water. I typically figure a ship is about 1/5 the density of water, so the actual ratio of volumes would be something like 160. Say you only want to lift half the weight, halving the submerged volume for the benefits you envision. So you need 80 times the volume of the ship for that gas, presumably hydrogen (well, nowadays helium is still expensive but it can be made available for a price in very large quantities--but if all the shipping in the world tried this plan we'd hit the limits of even modern extraction fast). The cube root of 80 is about 4.31--if your gas bag has the same proportions as your ship hull, that's how much longer and broader in beam this volume overhanging the ship would be.
The gas volume would have a huge sail area too; crosswinds would be a major problem. The bag, even if built lightly, would be a significant mass itself being extended over such a large volume, and yet, given the stresses winds would put on it, dangerously flimsy. That's quite aside from the risks of people shooting at it!
If the purpose of the exercise is to lower drag below the waterline, consider that the huge gas bag would have not inconsiderable drag in air of its own. I think you are right that overall it would be reduced, but you have to consider that offset--getting half the drag area out of the water will not halve the drag since you now have the gas volume's drag to factor in.
Much of the drag on a surface ship is wave drag, something that has no analogy for a free-flying airship (or a fully submerged submarine)--aircraft only have to worry about that if they go supersonic!
Might as well finish the job and build a proper airship and get free of the water completely.
Though to be sure, I've proposed my own version of an airship designed to be bound to the surface of the sea, most recently
here. The main economic niche I envision is to serve as a fast ferry. In NomadicSky's timeline, Cuba is ISOTed to our world from an ATL where it is a US state, so I was thinking Havana to Key West, but I've mentioned it in other contexts too--someone's "Nebraska Sea" Alt timeline for instance, for crossing the Sea from the Midwest to Texas.
I approached the idea from the opposite direction--take an airship, and anchor it firmly to the sea surface with submerged azipods that provide both directional control and propulsion. In my version the "ship" hull is entirely an airship, it has streamlined struts going down under the water and its engines are down there, but the bottom of the airship hull and any gondolas that might be suspended there are well clear of the wave tips, by meters or even tens of meters. Only a small amount of the ship's total mass is in water. Aside from the sheer HeliumHead wankery, the point is that it can go a lot faster than any conventional watercraft and is a technology that is older and less fuel-hungry than hovercraft or hydrofoils, the only vehicles I can think of in its speed class.
A society that could and would build these things would probably build more free-flying airships as well.
But I don't see either displacing most surface ships, and I don't think you can get any worthwhile benefit from lifting such ships partially out of the water with gas lift.