I'm up to 2544 now. That accounts for all paints with a unique name from every manufacture (i.e. one "Brilliant Black" from Mazda) and every seasonal event paint awarded up to this point, and a few duplicates names from the same manufacturer (i.e. two "Rosso" paints from Ferrari because I bought the passo corto after the Dino and it has a name--and color, it appears to be identical--in common). I don't have the 15th Anniversary paints.
Toyota
does have paints that are shared with Lexus, TOM'S and TRD, and they
do get their own slot in the list. The same goes for the Mine's BNR34 GT-Rs and their Nissan counterparts.
I don't know how many Polyphony believes there to be and I'm confident I don't have them all (due to my one-per-manufacturer rule of thumb), but I hope this is closer to what you're looking for.