I appreciate your concernes and so well founded. Once water penetrated in those holes, it will cause unseen major damage.
I would go to the home center and go to the shelving aisle and check out the brackets that you could mount to the window sill and support the window boxes. This way the fasteners and holes are in the sill which you could caulk out nicely.
be sure to leave an ample space between the back of the box and the siding so that the area can breath and not cause rotting.
Consider boxes made from pressure treated wood for rot resistance. Also drill holes in bottom so water can leach out.
Have the boxes lean alittle forward so that water will not fall on the siding and cause a black or brown area.