Here are some facts from my circumstances, take them as you will.
TL : DR I think it is very likely detection was made using a method that no weird stuff would prevent like has been suggested on these forums. Short of directly countering the method of detection preemptive, I think HB was screwed on this one.
1. I ran a private 32 bit bot on (made up number, for reasons) 10 accounts. It was a sloppily updated bot from a friends bot he wrote a while ago. It was pretty simple of a bot - it ran 3 separate bot task. Most of it was hard-coded as it was designed very specifically for those task for the 5 users or less who used it. The bot had a few different versions that I ran that hooked different ways over the past three weeks leading up to the ban, mostly due to me trying to mess with the code on my own. One of the hooks was _lua_load from endscene, the other hook was also on endscene, and the other hook was done in a way that I'm pretty sure got 5 accounts I used it on banned.. they got banned before the wave, actually..
2. I also ran another numbers of bots(lets say 10) running a very simple version in 64 bit of the bot. This had very limited, hard-coded task in it as I am clueless when it comes to RE work and I know it is a pain in the ass to RE stuff to 64 bit. However, a friend did enough of the RE work I needed to convert one of the bots task to a pure 64-bit bot, which I did for learning and fun. This bot also hooked multiple ways over the three weeks for the same reasons as above.
The results were 10/10 of the 32 bit bots running were banned, which is a good sign that the detection code/method used by who ever is working right now on Blizzard's anti-detection stuff only applied it to 32-bit. This makes sense, as HB was the clear intended target here. There are a couple of possible reasons for this result in my eyes.
A) I some how accidentally shared what ever code managed to get HB detected. No one knows for sure yet exactly what got them detected that I know, but I have a fairly good idea from talking to the person who did the RE work for the 64 bit functions for me for a week or so now, as he knows the entire code and how it works in the bot I was using and has looked into it a little. He has a good guess.
B) The '10' accounts banned were shared in the sense the gold-buyers who took the gold off of it earned every week then sent me money for what ever gold made could have possibly been using some kind of honorbuddy script to auto collect and mule the gold - causing them to be banned. The other 10 accounts not banned were my own personal new bot accounts that month with no one set up to collect like that, yet. I think it is unlikely as I've dealt with this buyer and done it this way for over 3 years now, with out any issues and we've exchanged 10's of thousands of dollars with out even sweating it. He swears he did not use an HB script or any at all and did it by hand. It's possible, but I find it doubtful.
Now, I actually personally talked to a member of the HB team who I will not name for privacy reasons on skype about this. I wanted to share the code of the 32 bit bot and all versions I ran of it over the past three weeks to perhaps help them narrow down the reason for detection if it was option A). Long story short, my friend who wrote most of the code has a personal dislike for him and asked me not to share any of his own code he provided me with him. I did not feel safe editing it down my self and not giving anything away as I am very noob at this stuff. I also felt like he was some what rude, arrogant, and made some pretty interesting post on these forums. As a result this exchange never occurred.
With all that said - should some one on the HB team wish to contact me via PM here that thinks they can benefit from the above information and would be fine agreeing to keeping everything private I share via a faxed, signed, legal document I provide I will do my best to strip down the code to what I can provide you which would include any code I suspect might have flagged the accounts and send it to your email of choice. It's totally over-kill and stupid, but it is the only way I feel comfortable doing so in my current situation - the friend of mine could face legal issues for even being involved in blizzard games.. and he would not be doing so with out my begging for it.