I had to run a DNS proxy to filter out AAAA records for any Netflix domains.
The norm seems to be for hosting services to contract with both HE and Cogent if they decide to go with one of them. This is why for typical client browsing you wouldn't notice--the other side has ensured you can reach them. HE seems to be the cheaper option, so people will route most of their traffic through HE, and then separately contract with Cogent for the smaller amount of traffic originating from/to Cogent networks. Alternatively, you contract with another network provider who handles that idiocy for you.
For sites that use HE.net and have more than one IPv6 subnet, I use the initial /64 for the DMZ, so that didn't matter on most of them. Small sites had just been using the /64 though, and I had to renumber those. Total pain.