I can just see miles of samurai, sitting in trees with war fans, semaphore-relaying "Adjust Fire!" out to sea...
Haha, its a game, I get it, I'm certainly no realism fanatic. There's minor kinds of historical inaccuracies everywhere, like full units of onna-bushi or ninja, but its more fun to have them in than not. At least they're based on some sort of historical fact, and you can even treat them in an abstract manner. Part of the appeal of the series is to throw you back into whatever era it is that they're making Total War out of and you expect the units and features to support that. Naval bombardment in support of in-land combat just feels like silly overkill - don't the poor samurai already have it bad enough against 'modern' weaponry, without weapons from the future? Let's just throw in the USS Akron and airborne-samurai from rappel lines while we're at it. At least the dirigibles are a realistic replacement for the samurai-in-trees as a forward observer.
Back then, naval bombardment meant pounding the crap out of seaside forts before they could pound you back, or sailing into harbors and using the threat of bombardment to take entire port cities hostage (Commodore Perry and the Black Ships). So the new port siege mechanics are a nice addition for that period.