It all goes back to capos. In mediaeval times (or even before), lutinists used capos that fitted on by being bolted through the neck and fixed at the back with a sort of butterfly nut. This meant holes had to be drilled through the neck & fingerboard; when not in use they were plugged, whence the spots. I guess that they nly had holes in some of the frets because it weakened the neck. Later, and with the introduction of instrument-friendly capos, the spots were used to indicate positions on the fingerboard.
Notice that classical guitarists don't use them, and get a bit sneery about people who do. Fiddlers are even worse; in the 18th century, the viol da gamba was a gentlemans's instrument (with frets); the 'cello (without frets) was a mere musician's instrument.
I don't know what the significance is of the actual positions of the spots today, if there is any; certainly the 12th and 5th are important on the guitar. I've seen some with a spot at the 10th fret instead of the 9th, and some with no spot at the 3rd or 7th.