ZeroTier founder here:
Clients accept identities learned from WHOIS via root servers, but not from regular nodes.
As mentioned in the writeup, this was reported and fixed rapidly. I don't think there is any remaining issue here, but I am doing a re-read and will publish a blog post in a bit.
It's also important to note that the original (fixed) issue also required a node to be offline for >30 days. So the attacker would have to know your network and the identity of a node that was has not been online for a long time and invest >$500K worth of GPU compute power (at current cloud rates) per identity target.
The certificate thing mentioned is well known and hasn't been considered a vulnerability because certificates of membership are not secrets. They are akin to the SSL server and client certificates presented on SSL connection. That being said, it wouldn't be a bad idea (defense in depth) to make it harder to get these to make enumeration more difficult. We're looking at some mechanisms for this in new versions of ZeroTier.