The main point is the sinusoids you are calling noise are at frequencies quite different from the frequency you are trying to measure. It sounds like you don't have much random noise that overlaps the frequency of interest.
The synchronous averaging (if I understood your explanation correctly) is the filter. You could do better in isolating the frequency you are trying to measure. But Filtering before the ADC would be where you would get the real benefit. Then you would be receiving more than just a few bits of the signal of interest.
But that doesn't only get rid of DC it attenuates other frequencies also. The closer they are to DC the greater their amplitude is reduced. Again this is essentially a filter and it is helping a little with reducing interference from lower frequencies, but you could be doing a lot better.
Your removing unwanted frequencies that your comb filter doesn't remove and that improves the SNR.
-jim
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