The number system is related to chords based off the diatonic scale of the key we are using. Not holes on the harmonica.
For example in G, the notes of the scale will be: G,A,B,C,D,E,F#,G and the corresponding numbers will be 1,2,3,4,5,6,7,1
Hence C is the 4th.
It does get a little confusing when some of these notes are dropped and changed for other scales outside the diatonic scale. This is explained more in the advanced section of the course.
In the meantime, just remember the G chord = 1, C chord = 4, and D chord = 5.