Splitting audio into bands and voiced/unvoiced content is basically how many "modern" low-bandwidth voice coding techniques like LPC, MELP, or CLEP work (see https://en.wikipedia.org/wiki/Linear_predictive_coding). The point of that processing is to compress, not encipher, the voice data.
Analog scramblers, like A-3, by contrast, shift the frequency content of the speech as the means of encipherment.
The point of the SIGSALLY voice coder is simply to keep the amount of key material for the one time pad reasonable. Even with that compression, each OTP record lasted only 12 minutes. MELP, which is a current DoD vocoder standard for use in secure voice channels, produces intelligible speech rates as low as 600 bps.
The part that is definitely a kluge is the key synchronization method. It seems that they did not use a PLL (which had already been invented by that point) to keep both ends in sync and instead relied on highly precise frequency references and turntables driven by synchronous motors with hundreds of poles.