There are a great variety of schematics for the harmonic percolator out there, and those caps are present on most of them, but are not on the ones I linked to just by chance. They
are on
Madbean's Pepperspray, and a
few others. I don't recall exactly what the impact of that cap is, but I remember that the effect is very small. Small enough that it might not be noticeable at all for your rig. Thinking back, I seem to remember that it reduced high frequency hash a little bit, and made the circuits sound a little smoother (which is not to say either one sounds smooth at all, because they definitely don't), but that could be a false memory or a flashback or something, so take it with a grain or two of salt.
Just remember that most of the (many, many) schematics that I consulted when making mine disagreed with each other, and then I tweaked them even more on the breadboard. The components on the vero represent what I thought sounded best with my rig and the transistors I had on hand, and probably don't agree 100% with any other schematic out there. You might want to consider adjusting yours to taste as well. If you're going to the trouble of making a new vero, I recommend breadboarding it first so that you know what you're getting before you build it. These circuits have a tendency to sound a little bit different with each build, even when you use the same component values, so I built mine with the specific components I used on the breadboard, except for the SMD.
Good luck with yours, I'm glad you like the circuit.