I suspect the cymatic patterns of were created using an ancient fabriel that replicated the "voidbinding" applications of Tension and Illumination.
Take for example Kholinar and Sesemalex Dar. Tension could soften the stone into a malleable form, and Cohesion could alter its shape into the protective windblades and canyons. This initially points to the Stonewards -- but the vast scale seems beyond the limits of the glimpses of what we've seen Stonewards accomplish, and the alignment with auditory resonance frequencies suggest Listener, rather than human application of Investiture. Specifically, Illumination. While human surgebinders use Illumination for Lightweaving, its application can also include "various waveforms", according to the Ars Arcanum. So... perhaps this is related to the the mostly as-yet-unrevealed "voidbinding" powers? That in turn points to the Dawnsingers, except we know that they weren't responsible for big undertakings, such as the excavation of the Palanaeum. Furthermore, the cymatic patterns seem restricted to the earliest portions of the Dawncities, and the means by which they were created was lost over time. Newer cities such as Yeddaw had to be deliberately excavated using shardblades. Much as an Oathgate accesses the surge of Transportation and amplifies it toward a singular purpose, a Tesnsion-Illumination fabrial might allow a single individual to liquefy the stone and vibrate it at the right frequencies to produce troughs and ridges. In some places (such as Kholinar and Sesemalex Dar) the original formations remain, but in most other cities they have been so eroded by Highstorms that the only indication of their existence is the overall layout of streets and buildings.
So, tying this all together, here's my theory: Sometime shortly before or after the start of the First Desolation, we had a human going around with a fabrial whose design was inspired by how Listeners were using the surges of Tension and Illumination. This human, with the assistance of a willing (but not Bonded) spren used the fabrials to create sheltering outposts that allowed humanity to expand their territorial presence outside of Shinovar.