Yes, they are in the convo log. I would prefer them to appear in the dialogue window as well. Another option would be to make the popups of "X+1" ontop of all other UI elements, but still, not always is the camera focused on the PC's during a modification so my personal preference is, as said, written in the dialogue box when it happens.
As for the OP-question, some do... some don't. For example the very first convo (after finding the book of the fallen victim) does. Killing a NPC then talking does. There are several other instances.
But yes, not all of them. Banter like "we leveled up!" or "I am so narcistic!" are just that, banter.