Nowadays they grow a new Penis on the arm if it has to be amputated, then attempt to attach it to the correct place nerve by nerve.
They don't work very well I am told, but I am certain that the GFFA had the technology to give him a new one.
The reason he has no penis is because Palpatine did not want him masturbating.
Palps was a bit of a prude and did not want him cheating on the Darkside (his new wife as confirmed in RoDV).