CATDADDY,
The short answer to your question is NO, product / box numbers do not distinguish traditional, scale, or Standard O rolling stock from each other in Lionel products. For other manufacturers, the story is somewhat different. With MTH, for example, any product numbered 20-xxxxx is probably going to be scale sized, but not necessarily scale accurate. Further, MTH rolling stock products numbered 30-xxxxx were originally equating to Lionel traditional size equipment, but then MTH started adding "scale" sized product to that line as well. Old K-line products had a numbering system that was supposed to distinguish between traditional and "scale" size, but I don't know how well that distinction was maintained. For purposes of this discussion, Atlas makes, I believe, only O scale sized equipment, but they maintain a numbering system that distinguishes between 2-rail and 3-rail equipment. 3rd Rail also makes O scale sized equipment that runs on both 2-rail and 3-rail track, but I don't know if their product numbering system reflects that difference.
Even those manufacturers that specialize in O scale sized equipment, as opposed to traditional or standard O, don't necessarily produce a true scale product because of the compromises required to run their equipment on both 2-rail and 3-rail track. Bottom line, only way to truly determine scale accuracy is to obtain product dimensions important to you and compare to prototype. For a lot of us, close is good enough.
Hope this helps a little.
Chuck