Yes, let's discuss why (all? most?) ships can't do that. And while we're at it, let's discuss this special ranged damage immunity that non-combat units (workers, generals) have. Because the embarked units are basically just another kind of these "defenseless" units. They generally take 4 hp damage from most ranged damage. Where this gets weird, is when I have a rocket artillery than can 1-shot (10+ damage) a STR-15-ish fortified pikemen unit, while I can only do 4 pts to the unfortified workers next to them... It doesn't pass any sort of reality check. I guess they wanted these units, particularly special people, to have a certain survivability because they're so valuable. I could buy it with the SPs, but workers or settlers? Very early on, when they're crucial, maybe they should be able to take 1 hit from < 10 STR attacks. But later in the game, they're easily replaced, so high tech should blow them out of the, err, land! I believe this is controlled by the NONCOMBAT_UNIT_RANGED_DAMAGE global define, which is 4. Meaning it's currently not possible to vary it by era, or unit type, or attack strength. I'd say at a minimum raise this to 5, so they can be 2-shotted.
Oddly enough I've been testing bombers lately and sometimes they blow workers up in 1 shot, other times they do the usual 4. I'm not sure why that is.
Another issue is with ship-to-ship combat. In most eras, the ranged attack is much weaker than the strength, and naval units defend using the strength value, it means that you typically do about 2 damage to an equivalent unit per shot. This drops even lower once they become damaged! It turns sea battles into rather long pea-shooting contests where you need 5-6 ships or multiple rounds to kill anything. That in itself isn't such a bad thing, but it's in marked contrast with the land combat, where most things do around 5 damage to their equivalent unit. It also makes it difficult to protect embarked units even with adequate escorts, because it takes the escorts forever to kill the enemy, while the enemy can autokill any embarked unit it's allowed to reach. Maybe this is a good reason why they shouldn't be allowed to one-shot embarked units - even with escorts, you could then ranged 1-shot the embarked units from 2-3 tiles away!
I've also thought about giving ships a 2-tile zone of control, but that's not moddable either.