See, in my mind they are incomparable units.
Cruisers hit more often than destroyers. So if you have the money for two cruisers or three destroyers, and you already have 100 submarines and 200 destroyers in your fleet, why not get the cruisers for the increased punch? It’s like buying tanks. Sure, 3 artillery is better than 2 armor, does not mean you don’t buy armor!
Also, I use cruisers a lot for shore bombardments. Transport + Cruiser + 2 Infantry means I generally take an island from one defender. As the Americans I can almost always afford a couple cruisers for behind the scenes. (not to mention, the odds of a fighter coming out and trying to hit your cruiser by Japan is far less than the same fighter attacking a destroyer. 17% higher odds of losing the fighter!)
What I am saying is, they are different units and you have to look at more than just cost and punch! There’s cost, punch, ability, what you already have on the board, etc. Now Battleships, for instance, could be compared to cruisers as they are virtually identical units in as much as they are used the same way, they have the same abilities, it’s just harder to sink a battleship. In that regard, I would say the cruisers are by far superior to the battleships (you can buy more, the off shore punch differential is negligible, and you can split them up.)