Because they have never done one, so there isn't any reason to expect it.

Because is Nintendo. Simple like that

they dont have the manpower in europe for a big event.

What does it matter? Sony and MS mostly showed what we already knew, and then some third parties/indies.

Nintendo does the same stuff over time with their Directs.

Is Nintendo even present at all?

Pretty sure they're at Gamescom, just no conference. 

Exactly. Nintendo hasn't had a conference at Gamescom for as long as I can remember, but they're always there in some capacity. They have a lot of playable stuff at this year's show too. Smash, HW, Bayo 2, Yoshi, Splatoon, Mario Party 10, etc.

I think they're also hosting a Smash Bros. for Wii U tournament there too if I remember right.

NoE restructuring. Plus they probably planned out what they will announce themselves over time

They always wait closer to fall to reveal their holiday plans. Microsoft and Sony use gamescom to finalize their holiday plans... bundles, final dates, etc. Nintendo waits until September. Just their style.

Also, as some have already said, they gave a huge unload of new games at E3, so there's no need for E3 1.5 from them two months later.

What is ridiculous is that your favorite gaming companies are now copying Nintendo...again...