Yes, the deformation analysis taking into account the cracked state in the cross-section is included in the concrete design in RFEM 6.
For this, the effective stiffness is calculated for each element in the concrete design according to the existing cross-section state of cracked (state II) or uncracked (state I), and then used in a second FEM calculation for the deformation.
In RFEM 5, this corresponds to the solution in the "RF‑CONCRETE Deflect" add-on module. In RFEM 6, this method is included in the concrete design.
Further information about determining the crack state as part of the deformation analysis can be found in the technical article at the following link.