Yes, you can increase the frequency. Check the top of SoftPWM.cpp
// 130 == 60 Hz (on 16 MHz part)
#define SOFTPWM_OCR 130
But be warned, it will eat into your available CPU time.
Theoretically, it can cope with many channels (up to something like 16 according to the site) without problems, but the more channels you have the less CPU time you have for other things. SoftPWM is hardware timer driven, so the flickering you are seeing may be caused by other interrupts taking priority, or interrupts being disabled at times, causing the SoftPWM to stall briefly.