In this case it is just to keep these areas from rounding out with the subsurf modifier.
There will be times when deleting faces will be for performance purposes, when modelling game assets for example.
With intersecting meshes, it doesn’t matter if the geometry is hidden, again unless its for performance, a very large scene is another example.
It really doesn’t matter, unless the intersecting geometry has faces sharing the same 3d space plane axis, Blender wont know which face to display and try displaing both which causes weird shading known as z fighting.
It comes down to the shape you are modeling, and your own OCD preferences.
And you will develop OCD’s when you have been modeling longer.
