I think the point is the bulbs are cheaper than the (a) cost of developing, deploying and tracking a one-off maintenance protocol change and (b) risk the instructions are applied to the wrong intersection.

This. And they rules may change, and someone might decide to turn them on someday. They are prepared then :)

It should be obvious if the light doesn't have ANY yellow or green bulb that they shouldn't be changed.

Usually we teach people to not try to be clever when applying checklists. More often than not the "obvious" thing to do can have fatal consequences.

Or maybe the last person forgot, or they were stolen, or whatever. You'd probably have to report that and waste the time of a bunch of people.

surely it is illegal to put up a traffic signal without working bulbs.

If the traffic lights on that intersection are off or go into that mode due to other reasons you'd have a yellow blinking light.