I think the crew and training costs are what bites. It's a sizable crew, and as touched on, the propulsion and other systems like the guns don't exist anywhere else. In the 80s, they had to bring in ww2 chiefs to explain to the ppl in the navy how things really worked, IIRC. Doing all of that for 2 or 4 ships is a heck of an expense.
*IF* it were feasible, you'd probably see a version of the VLS Mk. 41 launchers with armored hatches, I suppose. Replacing the Armored Box Launchers if nothing else. OTL planning envisioned *possibly* removing the aft turret for a more extensive VLS with hundreds of Tomahawks, etc. But by Reagan's second term the naval buildup was already losing steam and nothing more was done.