You can clip the springs... but I think the difference would be negligible. If you want to try it the general concensus seems to be about 25mm off the total length. I think Holeshot recommends cutting in their Stage 1 kits... but Ivan's kit & Factory Pro do not
Nylon washers may be better... they won't rust. They may, however, be thicker than the steel ones... so adjust accordingly.
I'd first run with the snorkel, and then without it... to see if there's any perceptible difference. I doubt there will be much if any... but if it seems to run better without it... then you could begin to try to start drilling some holes, incrementally. You want to drill them on the plane of the airbox lid that faces rearward. I personally believe (without any physical evidence to back it up) that smaller, maybe 1/2 inch holes are better because there would be less turbulence in the airbox than with 1" or 2" holes.
Basically though... 2 shims, 110 (or 112) main jets, A/F screws out 3 turns, and just removing the snorkel (no holes drilled) seems to be the ideal setup for most 2nd Gen B12 owners with a slip-on exhaust. I doubt that you'll be able to 'fine-tune' it much after that without really accurate dyno tests after each change.
My $.02 worth, anyway.