Hi Max,
The big difference between sinewave/square-wave clocks is the slew rate that can be achieved. Square-wave or clipped-sine clocks tend to have better slew-rate because of the decoupling of rise/fall time from the waveshape. Sine wave slew rate is given by 2π*F*Vpk, where F = input frequency and Vpk = peak amplitude. This can cause some trouble meeting the minimum slew rate requirements at lower frequencies with sine wave clocks, while staying within the input pin limitations on minimum and maximum voltage. I've included a graph that illustrates this effect.
The only other thing I can think of is potentially square wave clocks could couple higher order harmonics into CLKin1 through the shared power supply pin. If you're using an external VCO on CLKin1 and a reference clock at lower frequency on CLKin0, using a sine-wave clock source for CLKin0 can help minimize higher order harmonic coupling into the VCO signal (but you'll still get a spur at an offset equal to VCO ± CLKin0).
Regards,
Derek Payne
