How did that act prohibit Southern shipbuilding?
I will have to try and find where all the particular effects are explained in detail, but the Navigation Act of 1817 was not the only means by which the Federal government helped destroy Southern shipping and ship building.
One I remember is by giving US mail contracts to Northern shippers who could then add that money to their bottom line, while the Southern shippers would have to actually compete for the remaining shipping contracts.
I think this material is discussed in detail in that thread I linked to up above.