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At the end of Avengers: Endgame, when Tony Stark
snaps the Infinity Gauntlet v2, all of Thanos's ships also get disintegrated. The Chitauri Leviathans are living beasts, so it makes sense, but the Outrider Dropships are clearly mechanical, as seen in Avengers: Infinity War.
We did not see this with the snap in Avengers: Infinity War, where
only living things were dusted.
Why is it different this time around?
See 2m35s of this clip, ignore the Chitauri Leviathan in the foreground.
The Snap just performs the wielder’s will which is made quite clear over the events of Avengers: Infinity War and Avengers: Endgame. It’s made the most clear when Tony asks Smart Hulk what to do with his Snap.
Tony: You remember... everyone Thanos snapped away five years ago and just bringing them back to now, today. Don't change anything from the last five years.
Avengers: Endgame
Later on when Smart Hulk has done his Snap he again makes it clear that he had control over what the Snap did because he tried to bring Nat back.
Smart Hulk: You know, I tried. When I had the gauntlet, the stones, I really tried to bring her back.
Avengers: Endgame
Just to be complete Thanos’ Snap was only to kill half of all life and so that is why it didn’t affect ships or the like.
Gamora: The entire time I knew Thanos, he only ever had one goal: To bring balance to the Universe by wiping out half of all life. He used to kill people planet by planet, massacre by massacre...
[...]
Thanos: Little one, it's a simple calculus. This universe is finite, its resources finite. If life is left unchecked, life will cease to exist. It needs correction.
Avengers: Infinity War
The implication is then that Tony’s Snap was to destroy Thanos, his forces and equipment so that they could win the battle. A deleted scene shows Gamora is still alive and she was originally on Thanos’ side and so the Snap must have only been for those loyal to Thanos at the time of the Snap.
And of course the Snap can affect none living things as we see in all of the Snaps. In Thanos' first one it destroys clothes and "personal items" of those who are Snapped. In his second one he destroys the Infinity Stones.
Natasha Romanoff: Where are the stones?
Thanos: Gone. Reduced to atoms.
Bruce Banner: You used them two days ago!
Thanos: I used the stones to destroy the stones. It nearly killed me. But the work is done. It always will be. I am... inevitable.
Avengers: Endgame
Then in Smart Hulk's Snap he just reverts Thanos' Snap which brings back the clothing, personal items etc. Lastly, Tony's Snap affects clothing, ships and the like.
The snap is just the trigger to have the stones carry out your will, whatever it may be.
Thanos wanted to destroy half of all life so that's what happened. Stark wanted to destroy Thanos' invasion force which included their ships and technology so that is what happened.
There's no reason to believe the Stones aren't capable of eliminating non-living objects. When Thanos did his snap, it removed half of the population of the universe, yes. But it also removed their clothes, their smartphones, their nails and hair... all over the universe.
So yup, the Stones are perfectly capable of eliminating non-living stuff all over the universe, and they do what you tell them to do. Thanos wanted to eliminate half the life in the universe (including their clothes), Tony did what Tony wanted to do, which incidentally was on a much smaller scale (a few ships in close vicinity).
As a bonus, we've seen the damage a single Stone did in Guardians of the Galaxy - once, in the stories of how the Stones were used in the past (destroying entire planets), once in the destruction of the Collector's base, and finally, with the threat of what Ronan wanted to do to Nova Prime using just the single Stone (again, destroying the entire planet). We're led to believe that simply having the Stone touch the ground would be enough. We don't know if it would actually work and if the stories were accurate, so this is a side-note compared to actually seeing what Thanos actually did, universe-wide.
While it's true the Soul Stone and Mind Stone are related to characteristics of beings, that hardly limits the Stones' ability. They could dust a Plymouth Duster if you set your mind to it.
Further, it's not clear that "dusting" means "annihilation", in fact, the return of the Blipped suggests that they went into some sort of purgatory.
It's possible that Stark sent them back in time from whence they came, while removing any knowledge of the Time Heist. Since everyone who knew about Nebula'23's incursion was present there at the Stark Snap, that should suffice.
