ATSAM3X8E: Custom Arduino Due Design
My experience is limited to using rather than designing the "Due compatible" Duet board designed by Think3DPrint3D and RepRapPro using the same microcontroller, it uses 10pF external caps https://github.com/T3P3/Duet/blob/master/Duet0.8.5/Duet0.8.5_Schematic.pdf  digging around you could find the crystal capacitance pretty quickly, but as you and the other responder point out, if what you have works (and presuming the vast tranche of Due's work) then all's good.