A Tomahawk missile costs about $2M. A Mk 84 bomb is $16k for the "dumb" variant, and up to $35k in the JDAM version. It also has twice the payload.
An F-16 can carry 4 such bombs on one mission. Even when including the operating cost of the F-16, you can fly at least 5 missions, and drop 20 Mk 84 JDAMs for 40x payload using F-16s at the same cost as one Tomahawk.
Against targets that are well protected by enemy SAM's and fighters, the equation changes, as you correctly state. Flying F-16s direcly on top of S-400 batteries doesn't make much sense.
But then again, the S-400s themselves are not free, and if you can destroy the air defences at a cost that is lower than the purchase cost of those air defences, an air campaign is still worth it, even if it may need to be delayed until the air defences are taken care of.
I know I'm not getting the missile back, but the survivability of manned aircraft against a near-peer or peer-competitor may not that great...
Now that pilot may be reusable, but they also come with other challenges, like requiring 1/3 of an aircraft simply for pilot life support. They also get tired, sleepy, lazy, and cannot handle high Gs.
Then there is the logistic overhead of maintaining a re-used aircraft. Again, this has benefits, but for every hour of flight there are like 17 man-hours of maintenance. Plus you need mechanics, a fuel / parts / ammo / tools supply chains, runways, etc.
Ukraine is destroying billions of dollars in ships, planes and submarines with drones that surely cost a fraction of this.
Fast forward to today and big warships are still a thing, for one reason or another (mostly for fighting goat herders from Central Asia who don’t have access to torpedo-launching vessels), but the idea has remained the same. Of course that the very big and the very important US Navy will never get rid of their big warships, they’d rather sink praising Mahan until the very end than changing their strategic world-view (which would also most likely imply them losing their big warships jobs).
This wiki link about the French Jeune École is a good starting read [1]
Planes however were a huge threat to ships. Manually guided AA guns simply were not able to deal with them for a time, leading to situations like you said. Screening ships were not able to deal with them nearly as effectively. Modern surface to air missiles are at a point now where its a lot more of a fair fight, but as with anything, enough planes (or enough ships for that matter) will overwhealm.
Nowadays the main "meta" of naval surface combat revolves around anti-ship missiles. Over time destroyers have crept up in size, and armour has been all but abandoned as well. These new "destroyer" ships are enormous, with Arleigh Burke as an example sized comparible to 1900 heavy armoured cruisers. This allows them to carry a lot of anti ship missiles which are enormous.
This is because a large part of the counter strategy revloves around a few things. #1 - to be effective, you need to have several missiles timed to arrive at the enemy positon at once, to overwhealm their defence systems (CIWS and the like). Each defence system has a certain time taken and probability of successfully downing an incoming missile, so ideally you want both multiple defences on each ship (covering all incoming angles) and overlapping fields of fire (to catch any that leak through each individual defensive system). This synergises very well with multiple ships in close proximity able to cover one another with their defences, but they must be arranged carefully to allow a maximum of their defensive weapons to fire at oncoming missiles without blocking each other.
Small unmanned surface combatants may change this again, but to my mind the countermeasures are similar (layered fields of defensive fire, focus on defeating large incoming swarms using multiple overalpping systems)
Before things went mostly missile based, there were concepts for cheap, automated AA guns (even autonomous) - that stuff might just make a comeback.
But, yes, something will always go through, hence the strategy of destroying production facilities etc. But if defense is cheap and only little comes through the usefulness of drones drops again.
Note: this isn’t a theoretical future, the USA has been violating sovereign countries’ airspace and taking out those it unilaterally deems a terrorist, with collateral civilian damage, and threatens the International Criminal Court to not open any investigations
"The mechanical development of weapons, transportation, and communication makes the conquest of the world technically possible, and they make it technically possible to keep the world in that conquered state. Its lack was the reason why great ancient empires, though vast, failed to complete universal conquest of their world and perpetuate the conquest. Now, however, this is possible. Technology undoes both geographic and climatic barriers. Today no technological obstacle stands in the way of a world-wide empire, as modern technology makes it possible to extend the control of mind and action to every corner of the globe regardless of geography and season."
- Hans Morgenthau
So Oceania, Eurasia, and Eastasia?
On the other hand, the defender has an advantage if the enemy also can't inhabit a particular territory. If territory is guaranteed to become a no-man's land for both sides, that reduces the incentive to invade in the first place. Therefore drone tech should function like nukes, they increase the lethality of war but decrease the desire to go to war in the first place.