Just because a ship has unusual qualities, does not mean that it exclusively travels by relying on those qualities.
Harry Potter can ride a broom, yet he's also still seen walking and using the stairs.
The Flying Dutchman
The Flying Dutchman was capable of submerging (in At World's End, we find out that this is how you travel to/from Davy Jones' locker), but at all other times, the Dutchman sails like any other ship.
We never see the Dutchman submerge for different reasons, e.g. to quickly dodge cannonballs and then immediately resurface. It doesn't happen. Most likely, Davy Jones is only capable of traveling to/from the locker; without him being able to essentially use the Dutchman as a magical submarine.
Look at the final fight in At World's End, where the Dutchman and the Pearl clash in the middle of a maelstrom. At no point does the Dutchman behave like an irregular ship, it's essentially equal to the Pearl during this showdown.
As there is no proof that the Dutchman can do anything but travel to/from the locker by submerging, we can't assume that it's capable of any other form of unusual travel.
Furthermore, the Pearl is later shown to be capable of traveling from Davy Jones' locker to the real world as well, which proves that this travel method is not limited to magical ships.
Additionally, part of Davy Jones' shtick is that he promises the dead that they can keep sailing, under his command. Logically, he'd need to make sure that the sailing method used is as authentic as possible, in order for the sailors to actually want to work on the ship.
If the Flying Dutchman traveled on a magical cloud, steered by Davy Jones' telekinetic powers, there wouldn't be a reason for the sailors to stay.
The Silent Mary
First of all, the Silent Mary has no functional sails anymore. Those scraps are nowhere near enough to propel a ship that size (even when accounting for the lost weigh due to being hollow). Sails do not work unless they are attached on both ends.
In that sense, she already travels magically. And on top of that, she lacks quite a lot of her rigid structure.
Keep in mind that whatever keeps the Silent Mary afloat, also keeps the pirates themselves afloat (when they run on the water in order to get to Jack, who barely manages to flee to land on time).
For all intents and purposes, the Silent Mary does travel magically.
But why is that they need wind to sail or ship's wheel to divert direction ?
Why do ghosts still look like their pre-death human form, instead of taking an abstract shape?
Because it makes them recognizable. If every ghost in all media was represented as a wisp, that would get really annoying (and boring) really quickly.
Similarly, the Silent Mary has retained her looks to some extent, because there's simply no logical reason for her to change shape into anything else.
You also need to take into account the crew that operates the Silent Mary. Though they are aware that they are undead, their personalities have carried over from when they were alive. This includes how they operate the ship.
Keep in mind that the crew of the Silent Mary was essentially in purgatory, doomed to sail the Bermuda Triangle for eternity. Working off of that idea, it's the intention that the sailors still have to do the same manual labor, regardless of whether the Silent Mary stays magically afloat.
Incidentally, why do you think the Silent Mary needs to turn the wheel? It's just as possible that the crew simply turns the wheel to have an authentic feel of sailing. It's a very common trope that sailors are endlessly in love with sailing, so they'd be inclined to keep it authentic even when they don't need to.
There are so many similar questions that are pointless to answer, because it always boils down to "that's just the way it is":
- Why do ghosts, who are generally able to fly, tend to hover at a "normal" human height?
- Since gravity does not affect them, why do ghosts generally appear upright and not oriented differently?
- If they have no physical form, why do most ghosts look like their former selves?
- If ghosts have no physical shape, how are they able to speak? They have no larynx, nor lungs. And if they are magically capable of making sound, why do they still move their mouths?
- The same argument applies to seeing: how do they do it? If magically, why do they still use their eyes?
- And the same argument applies to hearing as well.
- Why are ghosts animated at all? Why not use a still frame? There's no functional purpose to their movement anyway.
Ghost are generally represented as an imprint of their past selves. It identifies them. It makes them recognizable.
