CircuitHub can autodetect parts specified as DNP for Altium projects.
To do so in your schematic you should set the type to Standard (No BOM). More details on this can be found here:
https://www.altium.com/documentation/17.1/display/ADES/Sch_Dlg-SchComponentPropertiesForm((Properties+for+Schematic+Component))_AD
This feature is not yet available for Eagle or KiCAD design although it is on the roadmap.