Which kind of shape function Midas consider for a beam with and without the flag "Consider shear deformation" in the section properties? 

Answer: 

Consider Shear Deformations is ticked on then, program will switch from Bernoulli beam theory formulations to Timoshenko beam theory formulations, where the extra shear component is taken into consideration. The beam element is formulated on the basis of the Timoshenko beam theory (a plane section initially normal to the neutral axis of the beam remains plane but not necessarily normal to the neutral axis in the deformed state) reflecting shear deformations.
PFA the document which explains the FEM formulations of beam element as per Timoshenko beam theory.