It's best to hone the cylinder. It will take all of the unburned oil and other varnish off the cylinder and help the rings seat. I generally hone the cylinder when I rebuild the top end.
On the other hand I've also done top ends where I was either to busy or lazy to properly wash the cylinder after honing so I didn't hone it. The bikes always ran fine and I didn't notice any power difference or excess blowby when the engine was torn down at the next top end.