Hello- I believe a 3" rifle aboard would have been a useful tool in some instances. The large bore Brookes and Dahlgrens that were the mainstay of the two fleets armament could not be depressed for firing below a nearby enemies waterline at the ranges many engagements took place. Though the turrets of the Federal Monitors were constructed with a thickness of 8 to 12 inches of iron, the decking was relatively thin 1 inch plate. A 3" bolt, well placed, could have pierced the deck. Whatever energy the bolt had after that feat would not have been conducive to proper operation of whatever was in the way.
The 3 inch rifle in wrought iron had twice the range of a 12 pounder Napoleon, with better accuracy at distance. The rifle would have been useful in engaging that weapon as it was frequently used by army batteries defending stretches of river.