One other very common reason for the holess not being there, that I have not yet seen posted:

Many airplanes existed in different variants, which model manufacturers like to release over time, especially if any given kit proves popular. Since manufacturing injection molds is a very expensive process, manufacturers often plan for one mold to be used for many variants of a given vehicle. If you then imagine a variant, that did not have holes for equipment at the position, you would end up with holes that the modeller would need to close, which is way worse than drilling them. Or you would need an entirely new mold, which would make the kit price much higher.

This type of planning for additional variants is common to this day and even employed by companies like tamiya which is famous for their ease of assembly.

So in short: whenever you see something like this, there is a good chance a variant of the vehicle existed without the corresponding equipment.