The absence of one kidney (unilateral renal agenesis) is much more common, but is not usually of any major concern, as long as the other kidney is healthy.
This has nothing to do with the infection but since he has only one the sooner the condition can be rectified the better for him.
Normally even if one kidney is damaged or absent a person taking much care can lead an almost normal life.
Once the cyst, infection id taken care of, there should not be a problem, unless he develpos any abnormal symptoms associated with the urinary tract.
Most contact sports would be advised against to prevent any possible damage to the one remaining one.
Adults with unilateral renal agenesis have considerably higher chances of hypertension (high blood pressure).