Are these changes done intentionally between revisions and is here a reason for it?

Without getting the translator on the line and asking them it's hard to say for sure, but it seems like the answer is no, it was a mistake.

"Flying with the Cannons" ("De Lucht in met de Cannons") is not a title of the translator's invention that he came up with to add a personal touch or because the Dutch translation of "Quidditch Through the Ages" didn't quite have the same effect as the original English. If, for example, the original title had been alliterative, then for sure, a translator might come up with a completely different title to maintain the alliteration, if a literal translation of the original could not be made to preserve it. However, that doesn't apply here. "Flying with the Cannons" is a completely different book in the Harry Potter universe that doesn't make its appearance in the original until The Chamber of Secrets:

The rest of Harry's Christmas presents were far more satisfactory. Hagrid had sent him a large tin of treacle fudge, which Harry decided to soften by the fire before eating; Ron had given him a book called Flying with the Cannons, a book of interesting facts about his favourite Quidditch team; and Hermione had bought him a luxury eagle-feather quill.

Harry Potter and the Chamber of Secrets - p.159 - Bloomsbury - Chapter 12, The Polyjuice Potion

In fact I don't believe the Chudley Cannons themselves even make an appearance until The Chamber of Secrets:

They climbed two more flights until they reached a door with peeling paint and a small plaque on it, saying 'Ronald's Room'.

Harry stepped in, his head almost touching the sloping ceiling, and blinked. It was like walking into a furnace: nearly everything in Ron's room seemed to be a violent shade of orange: the bedspread, the walls, even the ceiling. Then Harry realised that Ron had covered nearly every inch of the shabby wallpaper with posters of the same seven witches and wizards, all wearing bright orange robes, carrying broomsticks and waving energetically.

'Your Quidditch team?' said Harry.

'The Chudley Cannons,' said Ron, pointing at the orange bedspread, which was emblazoned with two giant black Cs and a speeding cannonball. 'Ninth in the league.'

Harry Potter and the Chamber of Secrets - p.35 - Bloomsbury - Chapter 3, The Burrow

So, by using "De Lucht in met de Cannons" the translation has brought in a totally different book which isn't introduced until later in the original.

What's more the mis-translation doesn't help in any way, it doesn't preserve anything in the original, in the way that a title which rhymes in Dutch, or is alliterative in Dutch might be used to translate a rhyming or alliterative title even if the meanings are totally different.

Also, the title of the book has no material effect on the events that take place, so there's no reason why you want to play with the title.

Furthermore, in England, a Comic Relief special version of "Quidditch Through the Ages" was produced, so writing it out of the translation seems like a bad move.

All this being the case, I think it was a plain and simple mistake.

And are such differences present in other translations as well?

Well, I don't know, but AcePL in the comments points out:

Polish book uses "Quidditch przez wieki", which translates back directly to "Quidditch Through The Ages"

Also, I myself have access to the Latin and Ancient Greek versions, though these were both Bloomsbury. The Latin uses: "Ludus Quidditch per Saecula" which translates nicely as "The Game of Quidditch Through the Ages". The Ancient Greek meanwhile uses (I think): "τὴν ἰκαροσφαιρικὴν ἐξ ἔτους εἰς ἔτος" which (I think) works out at "Quidditch from Year to Year" or something to that effect. So very much a translation of "Quidditch Through the Ages" and not "Flying with the Cannons".