Part 1 – Problem 05: The deliverable states that the assumption of flexible diaphragms with zero stiffness should be changed with the rigid diaphragm condition. Does it mean that for our numerical model in SAP2000/ETABS a certain thickness diaphragm should be introduced in order to satisfy this assumption ?

Because you are assigning rigid diaphragms rather than semi-rigid diaphragms, the thickness that you assign to the slab element should have little consequence on the behavior of the structure. Rigid diaphragms have infinite in-plane stiffness rather than considering the actual in-plane stiffness, so the slab thickness would not affect the behavior.