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While I dont have a Kobo for testing, I have no problems detecting any of my various other devices under OS X 10.11.4, and since the device detection code is common across all USB mass storage based devices, this does seem like the OS X update is breaking only some Apple machines. Without access to such a machine/device combo, there is not much I can do.
You will need to wait and see if Apple fixes the issue in their next update and stay with 10.11.3 in the meantime.
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