- What should be the value of the pullup resistors ?
This really depends on a lot of factors, such as the length of the wires you used to connect the sensor, driving strength of the pins, speed of transmission, etc. There is an excellent article on the topic: http://dsscircuits.com/articles/effects ... -resistors
- How do I check that my D1 mini is not damaged ?
- Could my GY-521 have been damaged too ?
It should be fine.
The breakout board that you are using has a voltage regulator that drops the 5V power to the required 3.3V for the sensor (it's the other black part apart from the sensor, the one with 5 legs). So it's quite correct that you powered the module with 5V.