I am not disagreeing that HDMI might be superior in some ways, but I think the answer is that USB works. And from an engineering and cost standpoint it would be difficult to make the case for using HDMI. More wires does not mean better, USB is more than capable of providing the bandwidth for hi-res audio.
As others have stated, HDMI connections have been popping up on DAC’s to accommodate I2S, not because it is inherently supported by the HDMI standard, but because I2S requires more wires to pass the signal.
I will step out on a technical limb here, so please feel free to correct me, but USB audio uses a packet protocol similar to most digital communications systems. Whereas I2S is a low level hardware signaling protocol meant to be used on short buses between hardware components. Is it better? Very possible, but it is totally up to the implementation, which for now has no standard, and may be prone to corruption if not done well. USB, by virtue of using a packet protocol has some verification capabilities to ensure accurate data transmission, I don’t know, but I am guessing the I2S signaling does not have this capability.
Back to the answer, they use USB because it works and makes technical and economic sense. Again, not disagreeing that I2S might sound better under the right circumstances, but if you ran the same packetized protocol on HDMI that you run on USB, there would be no inherent advantage, and it would be overkill.