I've never heard of a snake being fixed unless the reproductive organs were going to kill them.
The "incision" you are talking about it probably her equivalent to a belly button, some snakes keep a small slit where the umbilical cord was.

Also, these "nubs" are just the spurs, all ball pythons have them, some are just more prevalent than others, it is no way to tell if they are male or female. You have to get your snakes probed to tel the sex.

I would take Dopey out of the tank and put him in a tub, if you got him from petsmart and the other snake looked unhealthy, there's no telling if he has any diseases that might transfer over to Darla. I would also check both of them for mites.