Yeah, you're gonna want to keep a very close eye on any other babies. Inbreeding seems very likely and can cause other, hidden health problems. I wouldn't suggest breeding that pair again, you could end up with a lot of fatally malformed chicks or ones that, thanks to a weak immune system, catch and spread disease to the rest of your flock.
This guy, assuming he's otherwise healthy, should be fine with that foot. No need for intervention. Well- he'll be as fine as a crested duck can be with that deformed skull. The foot is the least of his worries!
If you want my honest opinion, don't breed crested ducks, ever. Stick with breeding animals that don't have a homozygous lethal trait and a major deformity.