If the array modifier isn't to be 'Applied' your best solution would probably be a straight out case of masking.
The clips above are using masks which enclose both (hidden) monkeys entirely so they won't be seen from any angle. If the cam is to be stationary however, a flat plane mask in front of each monkey should do.
Masking is a subject all it's own and beyond the scope of this question, but basically a mask is a flat plane or a cube or any object that will cut a hole into any part of the scene.
In our example monkeys 2 & 5 plus the green ground plane that's underneath and behind them will be cut out of the rendered output.
To replace the green ground plane you use the same camera to render a separate video of the ground only. (the monkey array and masks are temporarily removed or hidden)
A single frame would be all that's necessary when the cam is stationary)
Make sure to use the same codec for each render.
Both rendered outputs, the one with the holes and the one with just the ground, are rendered using (preferably) LOSSLESS video and those clips mixed in the VSE. The holed version must contain an alpha layer so the holes will be transparent, not black.
Rendering to a .png image sequence with an alpha layer is one option and it's default 15% compression still works quite well.
The ground plane version is laid into the VSE's bottom strip and the holed version above that. Set the latter's properties to "Alpha Over". (press N)
When mixed and rendered, the holes will allow the underlay (the ground plane version) to show through and there'll be no monkeys.
The same is done for the shadows. They appear on the original ground plane but won't be in the ground-plane-only version so when the masks are switched on, they'll disappear also.
A flat plane mask just above the ground is all they'll need.
Switching the masks on and off in the Outliner will switch the holes on and off. When on, the two monkeys and shadows will be cut out and disappear.