Everything else being equal, I would think it would be better to use several smaller caps in parallel. The smaller caps would likely have lower stray inductance, and lower esr (equivalent series resistance), both of which would then be further reduced by the parallel connections with the other capacitors (parallel connection reduces inductance and resistance, while it increases capacitance).
The only difference in phase effects that I can envision would correspond to the difference in stray inductance, which, although probably minimal, would be in the direction of favoring the parallel combination.
Regards,
-- Al
