Why does this 5V circuit use two of the EXACT same value capacitors?
It's not needing a larger capacitance issue considering 100nF is relatively small.
Here is the full schematic: Arduino Leonardo
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When you're using a decoupling capacitor like that you're trying to provide a low impedance path for transient current demands by your IC. The effectiveness of this is going to be directly related to the impedance of your decoupling capacitors, their mounting, vias, and "electrical" distance from your IC (the load that's demanding the current). By that I'm really talking about the inductance of the cap and all that stuff I just mentioned between it and your chips power pins.
This graph illustrates it nicely, capacitance dominates the impedance at lower frequencies until you get to the resonant point where inductance takes over.
Using two caps in parallel will give you a lower impedance path (think two resistors in parallel), allowing you to either draw more dynamic current, or giving you less ripple in your voltage when you do. Although you are still bound by the package impedance of the IC.