I did solve it, i was changing the cubes texture upon hitting certain body and the texture was being null, probably similar to throwing an exception and rendering it white. Once the correct texture was set the 2 seconds delay disappeared.
I also did turn off print statements in 2
_physics_process() of the game, prior to your suggestion and that gained me around 3 FPS.
As for your final suggestion, I think you are right, but what is the recommended value here ? surely setting it too high will have a strong performance impact, no ?
Thanks for your time @Zylann :-)