Good point with the Sub Bug™. I do fairly often keep my subs either in port, or covered by another ship, in part to avoid this, and in part because they aren't very good at defence. Sometimes I'm risky and send them out on their own. As to what's more economical, I'm not sure. Having big enough fleets to bombard is expensive in the first place, and aircraft carriers are not cheap. I will bombard given the opportunity, but I don't always have that many ships, and the carriers I have are usually for overseas land operations, at least initially. There's also the question of whether it's cheaper to replace lost subs or lost planes - it's true that I can make more planes overall, but it might cost more in hammers to replace planes lost to ship AA fire. In real life, air power is the way to go, in Civ, I'm not as certain.
I'd forgotten that in [C3C] Ironclads upgrade to Destroyers - they don't in Vanilla. That does make them a better deal, and might be enough for me to build them if they didn't have a new, separate tech. I suspect in most cases I'd still rather have the smaller destroyer force sooner by skipping Ironclads. Especially if I were already ahead in tech, I'd put up with only having Frigates and then pwning my enemy's navy with the first few destroyers I built after skipping Ironclads. It's an interesting idea that if I were out-teched, it might pay off to go Ironclads, build a bunch, keep them in port, and then mass-upgrade to leapfrog in naval power.