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The stock value of C6 in the SD-1 is .01uF.

The role of the capacitor is to roll off treble.

In its location in the circuit, a very small value cap of 100pF or even smaller is typically standard. Also, such a cap is really only needed if there is significant clipping occurring at that part of the circuit. In this particular case, it is merely a tone circuit with a relatively small "gain factor."

Also, the part of the circuit in question is essentially equivalent to a Tube Screamer, and there is no capacitor at all in that pedal.

If anything, it is an odd sort of "redundancy" on Boss' part, because there is already treble being removed by another capacitor. I think they "messed up" with that part of the design because the SD-1 was based off the OD-1. The problem seems to be that the OD-1 had no tone control, so a capacitor to remove treble would actually be helpful. But once the tone control was implemented, Boss made the mistake of leaving the capacitor in (and I think they made its value even larger!).

Here's another way to look at it - a pedal like the OCD is capable of creating much more distortion than the SD-1, and it only uses relatively tiny 220pF capacitors in the same location. Also, the tone circuit falls after those capacitors. And something like a Big Muff uses a huge 470pF cap at each clipping stage, and it has an insane amount of distortion and clipped treble in comparison...

So even if Boss went with a .001uF cap (or what is considered 1000pF), that would still be "ten times too big" the average size of 100pF. And - something like a TS actually uses a 47pF or 51pF cap, only where the distortion/clipping occurs (in the main drive stage, NOT the tone circuit).

The bottom line is that it was primarily a design mistake on Boss' part. It's easy to forget that the OD-1 predates the TS, and when Boss rolled out the SD-1, a tone control was still a fairly new concept with many pedals.