The opening paragraph of Dune reads
A beginning is the time for taking the most delicate care that the balances are correct. This every sister of the Bene Gesserit knows. To begin your study of the life of Muad'Dib, then, take care that you first place him in his time: born in the 57th year of the Padishah Emperor, Shaddam IV.
-- from "Manual of Muad'Dib" by the Princess Irulan
For this statement to work, for it to clearly define the year of Muad'Dib's birth, the reference to Emperor Shaddam IV has to uniquely identify exactly one person. This falls down if Shaddam IV refers to multiple people, or if it references someone not significant enough to be remembered by history.
Near the end of Children of Dune another quote reads:
"I do not have to be what my father was. I do not have to obey my father's rules or even believe everything he believed. It is my strength as a human that I can make my own choices of what to believe and what not to believe, of what to be and what not to be."
-- Leto Atreides II, The Harq al-Ada Biography
In Appendix IV of Dune, Selected Excerpts of the Nobel Houses, we read:
The Padishah Emperor, 81st of his line (House Corrino) to occupy the Golden Lion Throne, reigned from 10,156 (date his father Elrood IX, succumbed to chaumurky) ...
From these we can readily see the fact that Frank Herbert himself only "counted" rulers, and I suggest we're supposed to accept that this approach was common throughout the imperium. Elrood IX was an Emperor, as was Shaddam IV; Leto I was a Duke; Leto II the God Emperor.
(Aside: it's interesting that houses Corrino and Atreides address their rulers by their first name; house Harkonnen uses the house name instead - Baron Harkonnen vs Duke Leto.)
Paul Muad'Dib's first son, Leto, clearly didn't influence the pecking order. We can surmise that FH was influenced by our "real world" rules, and that this was because Muad'Dib's first son never ascended to rule, but (like most great authors) FH leaves much more unsaid that said.