Yes, this makes perfect sense.

The use of a half watt zener is pretty wimpy if his function in life is to cut off excess voltage. I imagine his junction vaporizes rather quickly in the event of excess voltage. It is now recommended by manufacturers to use uni-directional transient voltage suppressor or "tranzorb" or "TVS" to do this function. They look like and behave just like zener diodes but can take more of a wallop. The standard part for protecting TTL logic is the P4KE6.8A.

But, like lots of other things Williams did, they only went half way - they only put in half of the required protection into the circuit. This zener clamps the voltage to a lower and more acceptable value. If the voltage remains for a long period of time then the zener (or TVS) will vaporize and the clamping function will be gone thereby exposing the 7402 to this high voltage. The amount of time to kill the zener diode is only a few milliseconds. Williams should have put current limiting between the zener and the connector pin. Probably a low value solid state resettable fuse or "Polyswitch" would have been the best method. Not sure what the board replacement guys are doing to protect the input logic but hopefully they didn't just blindly copy Williams with this one.