Earlier quoted context omitted.
The article only mentions NAT as the most prominent example of middle boxes. And no, the UDP header obviously is not encrypted, if it were it wouldn't work with existing devices and OSes. UDP doesn't give you much information to mess with, which is part of why it's used for QUIC: it works through existing networks, and they can protect the deeper protocol layers against development of new middle-boxes attempting to l…
I am not sure it is that obvious given the article's focus on NAT. But what is the problem exactly then?
QUIC tries to prevent this by making as little as possible visible outside the encryption: it should look to a middlebox as much as possible like an opaque data stream, and not reveal any details about what's going on inside. Now there is a proposal to add something that is explicitly visible to the network, and people are worried that will come back to bite them in some way if they make an exception now.