Your are also right, you have to count this drop doing the Ohm's law calculation.But anyway, this book and these projects aims the complete beginner, who doesn't even know why using a resistor is needed. The first project is really simple but it is also a lot of information for the complete newcomer.Seriously, Arduino has developed so many stuff, do you really think they forgot to mention that drop ? Don't you think they decided not to mention it to make things easier to understand ?
If you want to be more accurate use a TVM (Transistorized Volt Meter) or as we used to have a VTVM (Vacuum Tube Voltmeter) to measure these circuits. The input impedance on these is more like 10 meg ohms. That will not load the circuit.