Can I keep my MBPR unplugged when not in use? If I shut down my MBPr and unplug the power cord every night then in the morning plug it back in and turn on the MacBook, will it have an effect on the battery charge cycles?
Only if the battery discharged to about 20% overnight for some reason it will count as new charge cycle.

For example if unplug at 100% and plug back in at 80% it is not counted as new charge cycle.