Does the MD-80 seat layout affect the balance of the aircraft?
The "D" seat is very near the aircraft centerline, and thus the roll axis. Since roll moment is the distance from the roll axis times weight, if the distance is small, the roll moment is very small. What roll moment is created can easily be canceled by a little bit of aileron trim if needed. 

The water tank on MD-80s is also placed on the LH side of the cargo. Full this is about 350 lbs, further from the centerline than the "D" seats. Also the LH side has an extra service door in the aft and the front LH door is larger than the R1 door, although the RH side also has the cargo doors.