Quick update
I installed the arduino board away from the EMC source and it seems to work perfectly, even with vibrations. After some research about EMC, the shielding is the last emergency solutions to protect against electromagnetic interference. It's advised to design properly the boards from the beginning to avoid these problems.
As this point, I assume that the arduino platform is not suitable for this harsh environment and I am in the process to switch to some industrial ecu. It's not even so expensive if you compare to arduECU rugged housing for arduino.
Thanks you everyone for the help !