I have had reasonable success adding the nozzle diameter to any internal hole radii. So, for a 10mm diameter internal hole printed with a 0.4mm nozzle I would create a hole 10.8mm wide, thats a radius of 5mm plus 0.4mm for the nozzle.
Not an exact art but often very close.

I think Slic3r and CURA both have the same issue where they seem to calculate the inside diameter of a hole as being the outer edge of the inner-most shell.
Much like drawing a small circle with a fat marker.