I'm no fan of Apple's App Store policies, but this one is entirely iFixit's fault.
Not necessarily. It's not clear that Apple's rules were reasonable. If the dev unit is identical to the production ones then an NDA is unreasonable unless it was only under NDA until an embargo.
It's not like iFixit went to a store, bought something, tore it down, and are getting punished for publishing the pictures. They got prerelease hardware for free (technically for a dollar plus sales tax) in exchange for an agreement not to talk about that hardware for a while. Then they talked about it anyway.
If you do accept it and violate it, be prepared for consequences.
This might well be the last pre-release thing they ever receive from Apple. So, sure, things aren't black and white, but they didn't exactly leave room for Apple to respond positively, especially given Apple's rather well known positions on leaked information.
100% absolutely "necessarily". Ifixit broke the rules, and got a light punishment for it. It doesn't matter how you feel on the matter, or if the end product is the same as the dev kit.
They broke the rules, and saying things like "Not necessarily" is reckless and an uneducated statement, which is simply not acceptable in HN comment sections.