Ok, I understand why you are confused about this. Please let's first understand how the elder wand works: the wand must be taken from it's owner against their will. This does not mean that it must specifically be disarmed. It can be snatched, summoned, taken after killing, stolen while dueling or any other way of taking the wand against the will of the owner. Grindelwald stole the wand from Gregorovitch, and I guess fired a spell in order to win the allegiance of the wand. Dumbledore won the wand by dueling and defeating Grindelwald. Now, Malfoy disarmed Dumbledore, thereby taking the elder wand away from its owner without their will. Snape killed Dumbledore, but this was pre-decided. Which means, that even before Dumbledore's death, the elder wand now belonged to Malfoy. So he was the owner of the wand.

Now neither Harry, nor Malfoy ever touched the elder wand, yet became its owners. So I am guessing here that winning the original wand from its owner would grant you allegiance to all their other wands. So, Harry won Malfoy's hawthorn wand. This means he also won any other wand that had their allegiance given to Malfoy, which happened to be the elder wand.

Now it happened several times in due course that Harry was parted with his wand. But it always ended up with him having his wand back. That means Harry's wand was never taken away from him. He always had it, in the moleskin pouch. Therefore, no matter who disarms Malfoy after Harry had taken his wand, it would not make any difference to the allegiance of the elder wand. Because it now belongs to Harry. So anyone wanting the elder wand must now win Harry's wand.

I hope it makes things clear to you. I am ready to edit or add to this answer any more doubts you have.

The Elder Wand

It is incorrect to assume that it is the Wand which must be taken, rather the previous owner must be defeated. It responds to power.

It is evident that Harry does not even get his hands on the Elder Wand until the Battle of Hogwarts - after he defeats Voldemort.

Harry snatches Malfoy's wand (as well as other wands) from his hands, at the Malfoys' Manor. At which point Mr Ollivander tells Harry that the wand now owes its allegiance to him (Harry):

“And this one?”
Ollivander performed the same examination.
“Hawthorn and unicorn hair. Ten inches precisely. Reasonably springy. This was the wand of Draco Malfoy.”
“Was?” repeated Harry. “Isn’t it still his?”
“Perhaps not. If you took it —”
“— I did —”
“— then it may be yours. Of course, the manner of taking matters. Much also depends upon the wand itself. In general, however, where a wand has been won, its allegiance will change.”
^{-Harry Potter and the Deathly Hallows, Chapter Twenty-Four (The Wandmaker).}

Prior to Harry disarming Draco, it is important to remember that Draco disarmed Dumbledore at the Astronomy Tower¹.

Harry explains this all to Voldemort in the last few moments before Voldemort gets killed; from Harry Potter and the Deathly Hallows, Chapter Thirty-Six (The Flaw in the Plan):

“Aren’t you listening? Snape never beat Dumbledore!
...
“You still don’t get it, Riddle, do you? Possessing the wand isn’t enough! Holding it, using it, doesn’t make it really yours. Didn’t you listen to Ollivander? The wand chooses the wizard. . . . The Elder Wand recognized a new master before Dumbledore died, someone who never even laid a hand on it. The new master removed the wand from Dumbledore against his will, never realizing exactly what he had done, or that the world’s most dangerous wand had given him its allegiance. . . .”
...
“The true master of the Elder Wand was Draco Malfoy.”
...
“But you’re too late,” said Harry. “You’ve missed your chance. I got there first. I overpowered Draco weeks ago. I took this wand from him.”

As per the second part of your question; Hermione disarms Draco after Harry has disarmed him. This has pretty much no effect since Harry is already the Master of both Draco's Hawthorn and Unicorn hair wand and the Elder Wand.

The wand definitely belongs to Harry Potter. J. K. Rowling says so in a FAQ entry on her old homepage:

Voldemort is also using the Elder Wand - the wand that is really Harry’s. It does not work properly against its true owner; no curse Voldemort casts on Harry functions properly; neither the Cruciatus curse nor the Killing Curse.

This is the part that makes little sense to me; why would both Malfoy's hawthorn wand and the Elder wand change their allegiance to Harry when only the hawthorn wand was taken from Malfoy's possession by Harry. Ollivander can be quoted in both film and book that the wand chooses the wizard, so in the case of Harry snatching the hawthorn wand at Malfoy Manor, only the hawthorn wand should have changed it's allegiance and therefore chosen Harry as it's new owner, while Malfoy remains the real owner of the Elder Wand when it is either destroyed as seen in the film or placed back in Dumbledore's grave as referred to in the book. This idea of Harry becoming owner of the Elder Wand is literally coming from the idea that a wizard or witch can lose all wands that have allegiance to him/her if they are defeated, when the only logical view would be that the wand held by the witch or wizard when he/she is defeated should change allegiance to the victor while any other possible wands allied to that same defeated witch/wizard continues with it's allegiance