They did and it has changed over time, mainly dropping some implied numbers and or some "separators". It makes looking for parts interesting since the coding is different for different time periods, e.g. pre-war, post-war, MPC, "modern". I am looking for the write up on it in one of my Greenberg reference books and will post a followup.
The material is embedded in other sections/books so I am resorting to Google.
Re MPC era:
It is very easy to separate the Lionel trains made in this era from all previous eras because Lionel went to a 5 digit numbering system.
As I find additional info I will try to edit this post.
Did Lionel have a system for numbering its products especially O scale rolling stock?
Looking back at your question are you asking for a definitive numbering cue to differentiate between scale (1/48) and "traditional (not to scale)?
Lionel started out making toy trains and "scale" per se was not a major consideration. The trains were designed/engineered to run on the track systems, aka O-27 and O-31. The trains were designed to look nice on the track and a lot of them used selective compression to achieve this. To make matter worse some of the equipment was "scale" but it was for older 1920-1930 era prototypes that were inherently smaller or the item was scale but not 1/48. At some point Lionel started using the term "Standard O" to denote scale items. While MTH did use RailKing for their "O-27" line, the Premier line is not always scale, except for the locomotives (usually). There are a lot of MTH rolling stock in the Premier line that is not scale and some 1800 era locomotives that are actually too large to be true 1/48 scale replicas.
