Now I understand why you were asking.
I think the "empty dusty bunker" issue would not arise in the normal course of events. I think the plan was to use the "protective" coal last. Another plan was never to be steaming around on the last shovelful of coal, so unless something very unusual had happened, I think those bunkers would be full.
I suggested that the protection afforded by the coal bunkers was theoretical, rather than practical, because I know of no action in which a protected cruiser actually was protected by shells bursting relatively harmlessly in the bunkers. If anyone else knows of such an action, I'd be very interested in hearing about it.
I envy you having a campaign. If your friend is insistent that some gesture be made taking protected cruisers' bunkers into account, how about this (which is totally off the top of my head, so I don't know if it works, and even if it does work, I don't know if it's worth the effort):
"Protected cruisers that have steamed less than 3/4 of their maximum range ignore critical hits caused by shells whose penetration die rolls were exactly the minimum needed for penetration."
The "3/4" is just a guess, but it probably should be something greater than 1/2. 2/3 is also reasonable.
If you're afraid this give protected cruisers an advantage without any corresponding disadvantage, how about this (accounting for those emptying bunkers and the potential for coal dust explosions):
"Hull damage caused by critical hits on protected cruisers that have steamed more than 3/4 of their maximum range is doubled."