If this is affecting you it's best to put a long TTL (at least 1 hour) on your domains. That way a good lookup will be cached longer and it will affect less people.
but last time io had a problem we continued to have downtime after it was resolved because of a high value for the SOA record :(
If I change the TTL for an A-record in Route53, how will that help if there is an NS-issue with nic-io?
(awesome if you could explain!)
Also, does the SOA and NS records have any effect here?
You could remove the delegation entries for the name servers that are returning results though, that might help.
This still doesn't rule out bad responses. As far as I know there's no way to achieve that. However, it will make sure correct ones stay active longer.
A high TTL on your NS records would be good as well for the same reason. On the SOA it shouldn't really matter.