I've just been looking at the following series of (I think) lithographs:
http://www.nytimes.com/slideshow/2014/01/30/opinion/30Myropticon-ss.html?emc=edit_tnt_20140228&tntemail0=y&_r=1
Will ACW gamers please get it right? It was the Monitor and the Virginia, not the Merrimac, which never fired a shot in anger. If you're keen on that miserable slaughterhouse of a war, the details matter.
Since the Union (the original owners) referred to the ship as the Merrimac throughout and the Confederates referred to it as the Virginia and the Merrimac (and occasionally the Merrimack) apparently at random and given the alliterative nature of the phrase "Monitor and Merrimac" it seems to me Merrimac is a perfectly reasonable name to use.
OK, if alliteration takes precedence over nomenclature, I'll call 'em the Santissima Trinidada and the Scharnhorst henceforth.
Since the ship was called the Merrimac by both of the states that operated her I'd say nomenclature was being taken into account.
Besides, the Union called her the Merrimac and the Union won and, as we all know, history is written by the victors :)