[1] https://www.documentcloud.org/documents/2714001-SB-Shooter-O...
Yes, there's a publicly available court order. How would you know there isn't also an NSL?
No, its not.
> I believe this kind of government requests
Its not a request.
> is usually made with a strong non-disclosure agreement
An agreement requires someone to agree. You probably mean a gag order, not a non-disclosure agreement. In any case, whatever you believe is normal is irrelevant: this is a public order, which was widely reported on before Cook's statement.
> So, either the consequences were not that bad or Apple has chosen to ignore them for the good cause.
Its clearly the first: there were no consequences for disclosing the order, since there was no secrecy provision attached to it and, in fact, it had been published and widely reported prior to Cook's response.
Or ... something "fishy" is going on and this article is just a bait by Apple to let its customers believe they do care about privacy ... while in reality the situation might be entirely different. And the "best" thing is that ordinary people will never know for sure, because with Apple's proprietary software philosophy, there is no way to tell.