Because they're not relevant.

I don't remember them ever doing a conference at Gamescom, maybe they did years ago but I don't know. They just do E3 and their own Directs instead of using these conventions.

Combination of not wanting to distract attention away from Hyrule Warriors and Bayonetta 2, NOE restructuring, and probably preferring to do something around TGS.

How exactly?

iwata and myamoto actually issued a statement why, they had a big staff meeting and everybody felt the same way. 

if you want to know the reason why nintendo excusitives didnt want to do gamescom breifing, here is what they said was their reason. you can find it here

No there isn't. Nintendo's attending, but they just have a booth there. They released a pretty long trailer of upcoming Wii U games yesterday (as well as a few that are out already), but it consisted of things they've shown before, nothing new.