I read a book a number of years ago but can't find it or remember the title (I thought it was Iron Giant - but don't think that's the case). Criminals have stolen a WW2 battleship (I want to say that it was based on the Yamato) and are causing havoc on the waves. Nothing modern can touch her, they try modern planes (modern pilots/planes not built/trained to evade flack) and ships (newer radar and missiles bounce off the hull) to sink it, so they dust off the Missouri and Idaho battleships to sink her. I think the criminal faction were stealing nukes. Google has not been my friend here.
It sounds as if you are just slightly misremembering the title; instead of Iron Giant I believe you are thinking of The Iron Man, a 1998 novel by John Watson (not to be confused with the work by Ted Hughes with the same title.)
The plot follows the theft of a Russian world War II era battleship, the "Stalin". As the OP recalled, it was designed to counter the Yamamoto and so has thicker armour and heavier armament than usual. In the course of the novel two F-15 attack the ship with no result, it shrugs off torpedos and missiles from the USS Jackson and so eventually two Iowa class battleships, the Iowa (not the Idaho) and the Missouri are pulled out of mothballs to sink it. The intent of the criminals was indeed to steal nuclear weapons, namely anti-submarine nuclear warheads.
If this is the book in question, then I doubt that it really fits as F&SF though.