What is the hand gesture Itachi does when calling Sasuke to him?
Itachi is flicking his fingers towards himself, not outwards (which would be shooing away someone), which was why Sasuke came over to him. It's called the Beckoning sign and it varies by country.
It's also not just an Itachi thing - it's a common gesture in Japan to call someone over to you. I believe it's a different gesture compared to Western countries hence the confusion, which is understandable since I also thought it was how the Western countries do it. Here's a video demonstrating the gesture: https://youtu.be/iBcQFBuj2Os
It's interesting to note that the 'come here' gestures of some English-speaking countries are considered rude in some Eastern countries and is even a ground for arrest in one country.
Some resources about hand gestures:

https://englishlive.ef.com/blog/english-in-the-real-world/hand-gestures/
https://www.tofugu.com/japan/japanese-body-language/