I had thought I'd already typed this post but apparently not. So apologies if this is a bit sketchy; I thought it up months ago and have probably forgotten some aspects of it.
In the Circe chapter of Ulysses, Stephen plays the piano. "With two fingers he repeats once more the series of empty fifths." I think it's because I'm a musician that I figured out the metaphor here. (I also have a blog for music thoughts.)
In music, a fifth is a distance between two notes in a scale. The distance between A and E in the A major scale (A, B, C#, D, E, F#, G#, A) is a fifth. To get a chord, you have three notes - a tonic, a third (or a minor third), and a fifth. A major is A, C#, E; A minor is A, C, E. (My terrible music pun is that A minor is ace.)
But what's interesting about Stephen's playing the piano is that it's only fifths. He's not playing a major third or a minor third in between the two notes. That's what I think the "empty fifth" means. The fifth is not colored by a major third or a minor third. A major third would sound happy, and a minor third would sound sad. This is neither; it's just empty.
I used the fifth from A to E to demonstrate all of this because I think Joyce wants the reader to notice that fifth specifically. Earlier in the novel, the other characters talk about a poet called A. E. They criticize his poetry for being dull and repetitive. The empty fifths - without the happiness of a major third or the sadness of a minor third - reflect that. A. E. the poet is boring; A to E the empty fifth is boring.