What were the disadvantages of early prop driven blended-wing aircraft?
Generally, to create lift means to deflect the oncoming airstream downwards. How and where this is done in detail on an airplane is less important than doing it with a smooth spanwise lift distribution such that the wake behind the aircraft is trough-shaped.
A fuselage is disturbing this lift distribution, but not severely. The length of the fuselage means that it creates considerable lift at small incidences, even with the low lift slope of slender bodies. In case of the N-250 it was found that an incidence of 2° produces the lowest drag. However, this also means that the lift is only just right at one angle of attack, and when the aircraft is flown in different conditions, the fuselage can mess up the lift distribution quite easily, especially if it is wider than necessary.
During the 1930s and 40s, when this was understood in detail not only in academia, but also in the design offices, progress in engine technology pushed operating altitudes up until planes needed pressurized cabins to transport passengers comfortably. Pressurisation demands a round or nearly-round fuselage cross section to keep structural mass down, so any attempt at widening and shaping the fuselage would result in an unacceptable mass penalty. This ended the experimentation with lift-creating fuselages.
As for the N-250, the idea of fuselage inclination in cruise is correct in theory, but resulted in massive protests from the cabin crew which now had to push their carts uphill, ending this kind of optimization quickly. This is why it never caught on.