I know the obvious out of universe reason for the discrepancy in the computing systems in the reboot universe and TOS universe in ST, but is there an in-universe account for the substantial difference in the computing systems?
Answer
The change in terminal interfaces on star ships must have occurred some time before Nero arrived in the alternate timeline. What drove the change is unknown, and will likely remain unknown. However, you can see that there are significant differences between the Original Series bridge and the bridge on the USS Kelvin.
Here we can see that the Kelvin has multiple large screens all around the bridge, view screens in front and random displays at the side/aft stations. Most controls, however, remain as individual key, switches and levers. 
Later, when the USS Enterprise's bridge is revealed, although the aesthetic has changed dramatically, interface-wise the biggest change is to replace the physical switches and toggles with touch-panels. There are still some physical manipulators, even at stations that wouldn't seem to obviously need them, such as communications (see the big sliding lever right in the middle of Uhura's panel). 
Thus, from the Kelvin to the Enterprise the only major change was from physical to virtual buttons, and some holographic display upgrades. Keep in mind too that it is unknown how old the USS Kelvin's bridge was, but at minimum we know that the roughly 20 years passed between the two bridge designs. In the modern world of computers that would more than account for the changes and improvements in technology (think of a laptop from 20 years ago compared to a modern one with a touch screen).
So, as I said earlier the change in computer tech started before the Narada arrived, it's cause is unknown at this time, and the cause is likely to stay unknown for the foreseeable future.
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