Quartus II - Can I include other files into a *.qsf file?
Tested with Quartus II 15.0

Its possible to add lines like these to the *.qsf file:

set LoadPinConstraints 1
source ../../constraints/DE4/GPIO.Button.Reset.sdc
source ../../constraints/DE4/GPIO.Buttons.sdc
source ../../constraints/DE4/GPIO.SlideSwitches.sdc
source ../../constraints/DE4/GPIO.LEDs.sdc


(These *.sdc files include pin assignments, I/O settings (voltage, standard, ...) and pin timings.)

But, Quartus will report a bad formatted *.qsf file with unsupported commands. After that, Quartus inlines all external pin assignments into the *.qsf file.

So yes it's possible, but the goal of modularization is gone.