Hi There,
Our son had hypospadias repair as a 9 month old. It was really scary for us, having him experience this at such a young age, though I think it is better to take care of this before they are too mobile. Depending on the extent of the repair, they won't be able to straddle anything for awhile so it is better to have the repair done earlier. Our first surgery didn't actually correct the problem totally so he had to have a fistula repaired again at 18 months and it was much, much more difficult keeping his hands away from the repair during diaper changes.
One thing I was surprised with was how terrible it is when they first come out of anaethesia. Every one I know who had a child undergo surgery told me how tough it was. Our son was almost violent; shaking and thrashing around; my husband had to hold him just to keep him still. I wouldn't hesitate to ask the nurses for some immediate pain management right after if this happens to you. I think they gave him some demoral, which helped calm him down. If the repair requires a catheter, you should invest in the next size up diaper as you will be double diapering so will need a larger second diaper over his regular diapers.
It also isn't fun keeping your child from having anything to eat for all that time. I nursed him right after the procedure, but he wasn't really interested.
All in all, the procedure is not an uncommon one, so the doctors should have experience and make the procedure a smooth one.
Good luck!