I see a bit of their reasoning. Taking from the article:

"When you have an environment with 20+ services, code sharing, maintenance and following updates become problematic. At Allegro we had the chance to find it out. It’s better to take out dependencies from business services as much as possible."

By adopting something like Hermes you are not really "taking out" a dependency, but abstracting it - as you said. Yet, by talking HTTP to the message broker you are abstracting away Kafka from your developers and your code. One less lib to depend on for each language you have in your architecture. One less version to control among your services, etc.