In appendix P of API650, Figures Figures P-2A...P-2F consider the Stiffness Coefficients for cases "Reinforcement on shell", so I understand that these figures already included the assumption that there is a tP= thickness of reinforcing pad plate (assumed =t)

Normally we should use the appropriate figure and "t" is "tank shell thickness at nozzle connection, exclusive of reinforcing pad thickness or extra-thickness of insert plate" (as is clearly stipulated in the original work Billimoria and Hagstrom’s "Stiffness Coefficients and Allowable Loads for Nozzles in Flat Bottom Storage Tanks").

Best regards.