Well I shall try and apply some logic to potentially an illogical situation. This won't be a definitive answer and is flawed on so many levels, but I thought I'd give it a stab....
Logically, keeping the clock as a separate entity from the rest of the displays allows the driver to quickly view the time safely with out having to decipher several pieces of other information on the screen (how this works when you want to look at the other stuff on the screen whilst driving I'm not sure - I did warn you this wasn't going to be a fool proof answer!).
Japanese culture is for digital watches / clocks. Logically this is what they build in to their cars?!?!?
Probably some one some where has decided that the LED type display that I guess you are referring too is the clearest and easiest to read (despite the fact it looks so bloody awful)?!?!?
Bugger it! In reality it still looks rubbish and out of place in the majority of vehicles that it is fitted to, so I haven't got a clue either as to why they persist with it.