I looked far and wide for a solution and I might've found it yesterday night:
Too many game captures. I had a scene full with game captures (50+) which I embedded into another scene where I got all my overlays sorted. Before deleting every game capture (I deleted the scene and started a new one with only one game capture) I had micro lags every ~2 seconds but never saw any spikes in my task manager. After deleting it my stream is smooth again.
Before I deleted that scene I also had micro lags even without using that scene, like when I was streaming my "just chatting" scene.
I hope this helps.
Hardware:
CPU: Intel i7-4770 @ 3.4GHz Quadcore (Haswell)
Motherboard: ASUS Z87-K, Sockel 1150, ATX, Z87
Grafikkarte: NVIDIA GeForce GTX 780
RAM: 32 GB DDR3-1600 (4x8GB, PC3-12800), Dual Channel
OS: Windows 10 Professional