The main difference between a runequest book and a heroquest book is the scope. Runequest games tend to play out as much more boots-in-the mud, conan-esque escapades where resource management is critical and combat is central. Heroquest games can theoretically cover the entire narrative range, but tend towards your Gilgamesh or King Aurthur type stories (or, given most adventuring parties, Team America World Police ). The books targeting each system cater to this to greater or lesser degrees, but there's usually at least a tone difference. In practical terms, this usually means that the heroquest adventures are structured with less combat and more handwavy "skill challenges" than in runequest. Eg, in Red Sun Rising, there's an entire adventure arc centering on managing a bunch of children building (sacred) sandcastles.
That being said, the HQ books are still absolutely 100% worth getting and reading. They're entertaining and informative, and a great basis to grab ideas for runequest games. Just don't expect to use the adventure paths without some tweaking. In particular, runequest doesn't have (as far as I know) an established method for handling heroquests, which HQ games tend to resort with some regularity.
Also, if you're not already aware of it, I also highly recommend picking up the Forgotten Secrets of Glorantha chapbook that Chaosium just put out a couple of months ago. Yeah, it's just a transcribed seminar, but what a seminar. It's pure sublime wonder.