I actually have many issues with the extended cut, and this is just one of them. Yes, Aragorn captures the ships in the novel, but in the film, it works much better for all of that to be omitted.

With the exception of the Faramir/Eowyn romance (which I'd have gladly lost a few minutes of the battle to include), everything else in the extended cut is unnecessary. We don't need more drunken hobbit dancing. We don't need yet more battle footage. We don't need Gandalf confronting the Witch King (not in the book, and actually makes no sense in terms of who is the more powerful being, hence why Jackson probably cut it in the first place).

Regarding Saruman's fate, it either should have been seen in The Two Towers, or not at all, as it is an unnecessary and irrelevant loose end in Jackson's version. This is because he chose to cut the critical Scouring of the Shire chapter - understandably, as it would have been too episodic and much less of a big deal following the big climax with the destruction of the Ring and the crowning of Aragorn. In the novel, Saruman escapes and goes to the Shire, where he ravages the land and causes a lot of trouble that the hobbits have to deal with when they return. Saruman is ultimately killed by Wormtongue, on the doorstep of Bag End.

Also, the Mouth of Sauron sequence is entirely unnecessary. In the novel, it works because the way the story is structured, the last we heard of Frodo he'd been captured by orcs following the encounter with Shelob. In the novel, there's a genuine sense of despair when the mithril coat is shown to Gandalf and Aragorn, because it appears Sauron therefore has the Ring. But in the film, because it cross cuts between the different characters, we already know Frodo still has the Ring, so the scene becomes a dramatic irrelevance.