I like this idea too.
But how about this for a slight deviation: a Naval Base fires once at every
Cruiser and Battleship in the invading fleet and any scores of a 1 merely prevent that ship from conducting Shore Bombardment - but the invasion still goes ahead anyway, i.e. Transports still unload. Not so harsh as damaging a Battleship or sinking a Cruiser. This would make the coastal defences more of a deterrant than a deadly threat.
As well as that, perhaps any 1s scored against invading Transports just prevent those Transports from unloading this turn? In this case the attacking player would still have to commit any un-hit Transports to the embattled territory. Or perhaps this is too harsh? Just some ideas.
What we need
is a dedicated Coastal Artillery/Fortifications piece. Then perhaps it could work in conjunction with a friendly Naval Base in the same territory that is under Amphibious Assault, using a combination of deter/kill abilities.