I believe there this could be traced back to the so-called downwash angle of the air coming off the wing.
Looking at the picture below (and put on some imaginary engines on the back like the DC9/MD80), it becomes clear that by mounting it upwards by a few degrees would make it meet the airstream at the streamline angle:
You would want to that streamline to interact with the aircraft fan blades with the wind at the same angles. I would imagine that if you did not do this, it would result in an uneven force on the fan blades, which would probably be highly undesirable.
Looking at the drawings of the DC9, it might appear that the shorter version has a higher angle, and that the longer version has a smaller angle, as further from the wing the downwash angle is less, as could also be seen above.
For a little further analysis, the following is apparently off the DC-9 Manual, and might shed a little more light on the design, in particular in the last paragraph:
"The nacelles have been designed to enclose the JT8D engine with a
shape that will allow the highest installed performance ( thrust minus
drag ) possible at all flight conditions. The nacelle nose cowling is
nonsymmetrical to keep the drag to a minimum at the high mach number
The nonsymmetry is required to maintain an extremely flat nacelle line
adjacent to the fuselage, such that the nacelle supervelocity
increments, when added to those from the pylon and fuselage, do not
lead to super-critical velocities with resultant shockwave losses.
The nacelle axis and pylon have been set at 3 degrees angle of attack
relative to the fuselage to align them with the local flow conditions
prevalent at cruising conditions. This is necessary to eliminate the
interference and high induced drag that they would otherwise be
subjected to. The nozzle is then canted upward relative to the engine
axis, thus eliminating the pitching effects due to thrust."
Following picture appears to show the nozzle angle is in fact more horizontal than the entry angle, with the underside longer than the upper side:
Thus, while it might not aesthetically pleasing maybe to have it off by a few degrees from the fuselage body, but it does bring advantages when seen with the airflow, and resulting concerns about that the thrust is not being vectored along the body axis is corrected by the nozzle.