The only way I know (I just started learning Blender a couple of weeks ago) would be to apply the modifier and modify the mesh manually.
Maybe there are some addons which offer such feature.
No, because they’re not objects. The modifier affects the object data (mesh, splines) of one object, it doesn’t produce multiple objects. The options to get rid of one are:
Apply the modifiers
Hide or cut the mesh with another modifier after the arrays
Make the distribution with something else than array modifiers. Procedural duplication, or particle system
Wouldn’t a boolean Modifier after the arrays allow you to subtract the unwanted window? Just make a cube object to encompass the unwanted window(s) and set the boolean to subtract. Shouldn’t be any need to apply any of the modifiers.
If you want to reduce load on your PC I would recommend alt-duplicating the objects. This will be faster than a array modifier, and will easily allow you to remove one, and should not be too slow to set up.
Yes, with or without applying the modifier, as the modifier result is used either way. But alt+D doesn’t create what is called an instance in Blender. It creates a linked duplicate
Linked duplicate doesn’t reference the whole object, only object data.
An instance references the whole object. Instancing options are:
procedural duplication: dupliverts, -frames, -faces, -groups. Dupligroups are also known as group instances
particle system duplication
linked libraries
Object data might be the most significant part resource-wise depending on your scene, but it’s not the same. Since linked duplicate doesn’t reference objects, you can use different modifiers on them, which in turn modify the original referenced data and gives you different results with new resource requirements.