Your hunch was correct.
I plugged in USB devices in all USB ports and the issue went away.
Then I started to unplug them one by one and I noticed that the problem is 
related only to one of the 3 external USB ports.
As soon as I unplug the device from that USB port kworker and ksoftirqd will 
instantly start to abuse the CPU.

USB devices:

$ lsusb
Bus 004 Device 006: ID 0cf3:e005 Atheros Communications, Inc. 
Bus 004 Device 002: ID 0438:7900 Advanced Micro Devices, Inc. 
Bus 004 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Bus 003 Device 004: ID 06cb:75bf Synaptics, Inc. 
Bus 003 Device 003: ID 0bda:0129 Realtek Semiconductor Corp. RTS5129 Card 
Reader Controller
Bus 003 Device 002: ID 0438:7900 Advanced Micro Devices, Inc. 
Bus 003 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Bus 002 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub
Bus 001 Device 002: ID 0bda:5684 Realtek Semiconductor Corp. 
Bus 001 Device 008: ID 0458:003a KYE Systems Corp. (Mouse Systems) NetScroll+ 
Mini Traveler / Genius NetScroll 120  <== I connected a mouse to the USB port 
that I mentioned earlier
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub

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https://bugs.launchpad.net/bugs/1488426

Title:
  High CPU usage of kworker/ksoftirqd

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