I've had 4 runts so far and all have fed on live hopper mice (a little on the small side but with open eyes and long fur) right after shedding. The first two where twins brothers in the low to mid 30s gram range back in 2003. The last two where from a disastrous first clutch this year (3 slugs, 2 infertile, only 2 fertile). Of the two fertile eggs one was a "light bulb". However, I was very surprised that even the good looking egg had an extremely small baby (they where small eggs, they just didn't look that small). The babies where in the low to mid 20s grams - the smallest I've ever seen. Both ate last week right after their first shed and considerably increased their weights. In fact, the female ate both the hoppers this week so I need to go out and get another for the male. I'm sure a lot of it is gut load but she is already up to normal hatchling weight in just a couple weeks.
So, my LIMITED experience is that runts aren't a problem and it only puts them a few weeks behind non runts. I've occasionally had some slow starters but none of them where the runts. I did have a baby leave it's yolk behind once and it was a slow starter and had me worried but he eventually started eating and is doing fine now.
I’m even interested in selective breeding for clutches with more and smaller eggs from ball pythons based on my opinion that runts don’t make much difference in captivity but it’s starting to look like the tendency to lay larger numbers of smaller eggs isn’t as genetically predictable as I originally hoped. I’ve seen two cases where a first clutch might come out with a high ratio of eggs but then the next clutch goes to the other extreme.