It will depend just what you are trying to decide based on the "nominal thickness".
My experience is that the cladding is only for corrosion allowance, and thus UCL-23(b) applies. This paragraph recognizes that if you order 39 mm composite thickness with 3 mm of cladding the actual clad may exist within the 36 mm base metal thickness, but this is permitted for a "reasonable" amount of cladding without any reduction in the base metal allowable stress even when the cladding material is weaker.
For selecting the PWHT, UCL-34(a) only requires the ordered base metal thickness to be considered. For deciding if the base metal requires impact testing UCL-27 only requires considering the ordered base metal thickness.
The mills will supply and price the material very differently depending on how you specify your thicknesses. For instance, SA-263 para 11.4 permits much larger overruns on clad plate than SA-20 para 14.2. This may not matter on a single small vessel, but can have significant impact on multiple shop built vessels or a large, field erected vessel (extra welding, shipping and lift weight, etc). You can specify nominal thickness (underrun permitted as per the standard Code rules) or minimum thickness (extra $ and weight) for either the base, clad or composite thicknesses. You can specify base thickness plus clad thickness, or composite thickness including clad thickness.
Weld procedure selection for the base metal will only depend on the base metal thickness, but my Code knowledge can't point you at the applicable paragraphs.
Part UCL will be your guide on most items.
Good luck
Geoff