-If the button sensor is on the top layer, can I have something, like the CY8CMBR3108 beneath it, or does it needs some clearance?
1. For different layer, clearance is not required but is recommended. In addition, It is recommended to make sure sensor trace and communication trace(e.g. I2C trace) are vertical if they are on different layers.
-I want to ad some LEDs for feedback, is it possible to put 2 in the middle of the sensor ( soldered on the bottom, facing a hole)? If I want to add other LED on th side, with the same technic, what is the minimal distance from the side of the sensor I can go?
2. Generally, >2mm is recommended.
-If I understand well this document http://www.cypress.com/file/41076/download page 81, a hatched ground must be present on layer 3, and on empty space of the bottom layer, but what about the top layer? Do I need an other hatched ground on the top layer with clearance around the sensor?
3. Yes. Hatch ground is recommended on the top layer with clearance.
-Can I use the 3rd layer ( aka the ground layer I think) for rooting the non-capsense traces ?
4. Yes. You can.
Hope it can help you!