It definitely does affect the payments, and if ou have a detailed surface scanner it boosts them even more
Decided to assess the value of individual scanning
If you have a Detailed Surface Scan then I believe the value of the data varies with the composition of what you find as well as the quantity of scans done. I do have one and the numbers below are the results of using it
Unexplored system, initially discovered 18 bodies including the star - No value checked
Scanned a total of 8 bodies including the star - 8885
Discovered an additional 9 bodies - 11338
Scanned an additional 4 bodies (one with high metal content 33%) - 15358
These were around and included a second start in system
As you can see there is additional credits for detailed scans at least, the return can be substantial but if the system has multiple stars it may not be cost/time vs return effective. As a bonus the station around the second star has some excellent equipment, got an A2 fuel scoop that maxes out at 75 per second.