Completely up to you. I have never bolted any box together except my current hutch being bolted down to the work surface. For just a top / bottom, there's usually enough weight of tools to keep anything from moving around. I'd not be concerned unless it where a tall / narrow type of box.
Never even thought of drilling holes in my tool box.
I do move my Snap-on top box from one to the other, between garage and mancave, depending on where I'm working.
If not bolted down you can take it in the truck to jobs.
Unless you move it all the time on uneven floor or have security issues I wouldn't. Even then it could be a double edged sword. Bolting them together raises the CG of the bottom box. If the box does tip and they are bolted together you are toally screwed. If they are separate and they tip you have a change, slight, to save the bottom.
Never even thought of drilling holes in my tool box.
I do move my Snap-on top box from one to the other, between garage and mancave, depending on where I'm working.
If not bolted down you can take it in the truck to jobs.