I was hoping I wasn't the only one in this situation (not for wanting to wish ill upon others, but just to find that it isn't a more confusing, unique issue!), so this is good news that I'm not just crazy, haha.

Both my boyfriend and I are legacy members that originally purchased the 1.0 Collector's Edition. He subscribed and started playing much later in 1.0 than me, but that's the only difference... He ended up receiving his 2.0 Collector's Edition bonus items with no issues.

My Mog Station account, on the other hand, is reflecting the same errors that all of yours seem to: the Onion Helm is there, but it's asking me to upgrade to 2.0 CE for all of the new bonuses.

I submitted an email ticket about 5 days ago, now... It took SE over 24 hours just to respond with an automated email that said they received my ticket (better than nothing, but odd that a fully automated one would take that long, even considering traffic). If I'm able to catch the live chat up and running in the next couple days, I may just do that. I just didn't want to nag them since this isn't an immediate issue for me (as long as we get the items eventually...).