I think the OP meant that the "Strength" property is the same on the 2 ships. It might be, I cant recall, but as pointed out HOW that strength is applicable (ranged vs melee) makes them very different.
One thing that does seem out of balance is the defense of the BB vs the Missile Cruiser. MCs seem much harder to sink than a BB which makes no sense (even ironclads sometimes seem more difficult!). The 2 things which defines a BB are a) big guns and b) thick main belt armour . Cut back on the armour (typically to make it faster) on a BB and you have a heavy cruiser.
The MC seems to be the least realistic: tougher than the BB (hence it must have a bit more armour) but still faster. Add the fact that it can carry missiles in addition to it's native ranged attack and it seems pretty fearsome.
...and I really dont like that you can see exactly what type of missiles each of them is carrying.