On that version of Hyper Cache a compatibility check has been made for WordPress 4.0 and an important fix added: the cache (wrong) cleaning while working on draft posts.
I’ve been reported of worse performances of Hyper Cache 3 versus Hyper Cache 2. It may be but Hyper Cache 2 was no more compatible with the new WordPress comment pagination, post types and so on. Version 3 is, but there is the possibility that this comptibility lower the cache performances.
Anyway, I HAVE NOT EXPERIENCED that problem on my blogs!