I was thinking about an upgrade of my 24-fret RG guitar. Even though it's a «shredding» piece of instrument, I wanted to set up low-output pups on it, but then… some guy told me that this long neck will worsen the sound of the vintage-output pickup in the neck position. Is it true? Will 20-22 fret guitar with the same body sound differently that much? Especially speaking about low-output pups in the neck, if it matters.
tl;dr No - that guy is talking nonsense.
It doesn't matter how many frets there are as far as the strings go - the first 22 are still in the same positions on both.
The one thing that may change if you alter a guitar from a 20 to a 24 fret neck is the exact location of the neck pickup:
If you have more frets, the neck pickup will need to be closer to the bridge, and this will actually change the sound, as the frequencies picked up at greatest amplitude vary along the length of the string.
Whether or not that worsens it or improves it is entirely down to what you like, but there will be a difference, yes.
In your case, however, this is almost irrelevant. You have a 24 fret neck and simply want to replace your current pickups with low-output vintage pickups. This will provide a difference in tone from the pickups that far outweighs any difference between locating the pickup in the usual place on a 22 fret guitar.