In that case, the only plausible explanation is that they deliberately crippled the SD card slot so that the 1DX with its dual CF slots would look more valuable by comparison. Which is just sad.
I find that implausible. I can think of zero 1Dx owners who would have instead bought at 5D3 had the second slot been faster. Canon knows its market pretty well, I doubt they thought for one second that a UHS SD slot in the 5D would have eaten away any 1D sales.
Disabling things in firmware (like AFMA in entry level cameras) could be a crippling-to-drive-higher-end-sales move. But the speed of the second slot in a camera which costs half as much... I just don't see that affecting sales one bit. The 1Dx sells because of speed and build, not because its second slot is CF as opposed to slow SD.
Practical reasons could include things beyond timing. Maybe the second slot was not a priority and they decided to burn down their stock of older components. But "let's make the second slot in this camera slow so that our $7,000 model with its 14FPS mechanism, RGB metering, three processors, weather sealing, dual batteries, 1/250 flash sync, 200k ISO, etc. looks a little better" seems as unlikely as "they didn't know about UHS."