9th, 11th & 13th chords should still have 5ths in them. If I wish to omit the 5th, that should be up to me. 9ths are supposed to be 1, 3, 5, 7 & 9. 11ths are supposed to have 1, 3, 5, 7, 9 & 11. 13ths are supposed to have 1, 3, 5, 7, 9, 11 & 13.
Seriously, it’s annoying.
I’m not a developer here but they explained this to me once, something to do with simplified 4-note chord voicing to keep it from sounding too dense and cluttered. I’m not 100% clear on the music theory concept (and it’s stupidly hard to find a good source online) but something about how the most essential parts of an extended chord are the 1, 3, and 7 notes. So a 9th chord would be 1, 3, 7, 9; a 13th chord would be 1, 3, 7, 13. Not sure why an 11th chord turns into a slash chord with 1, 7, 9, 11 (e.g. a D11 would be C over D), but it’s common for songs to use that chord (though often they have the 5 too, so it’s a shame that note gets omitted in Hooktheory, and therefore I understand your frustration.)
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I mean, alot of songs might not use the 5th (so Hooktheory should accurately omit 5ths for those songs) because it sounds cluttered but it naturally is part of the scales so it makes sense to be provided as an option.
the fifth is only necessary when there is some alternation to the fifth (i.e. flat 5 or sharp 5), usually the fifth is omitted because it makes the chord sound “muddy” or “cluttered”.
Hookpad omits the fifth for this reason.
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At least it’s not GarageBand where the 1 is omitted from 9th chords. Yes, for real.