My son recently had hypospadias repair and now has a cyst close to the incision. Is this an emergency?

No, unless can't pee. Hopefully this is a small epidermal inclusion cyst which can easily be removed at your convenience, unless your son complains of pain or difficulty urinating. A urethral diverticulum, or outpouching can sometimes be mistaken for a cyst. This would better be corrected sooner rather than later.
No. No it is not unless it is inflammed, angry looking and painful, or in other words it looks like it is infected.