It is a big decision. If you haven’t already, I strongly recommend that you get on each sized bike and test ride them. In years gone by I would almost always recommended going with a size up, but now with the longer “reaches” on these more recent frames, I do not think that’s such a good rule of thumb. The models of Kona bikes that I have read up on seem to have longer reach measurements, but I don’t know on the Honzo. Hmmmm. At 5.’6″ I would generally think that you would do better in a medium than a small for most bikes. Of course if you have test ridden both bikes and feel like you are going to need a long stem for the small frame, then I would move up to the medium frame and go with a short stem.
If it’s not too late- I’m 5′ 7” and I ride a medium 29er. The medium fits perfect for me, if not slightly too small. I could probably push it to a large, but I like bikes to run on the larger side. Many of the small bikes, even 29ers, that I’ve ridden felt almost like kids bikes. As a fellow 29er MTBer with a similar height as you, I’d would think the medium would be better.