We do see a few things about the naming system throughout the series. Firstly, as you've mentioned, there are definitely Yeerks with the same name, and different numbers.
Secondly, we very rarely see any Yeerks with more or less than three digits in their numerical designation, with the Visser and his twin being the most obvious exception. We're not entirely sure how many Yeerks spawn from each set of parents- I'm under the impression it's in the "hundreds" range, rather than the "thousands" (though I am missing any exact quotes to this effect at the moment). If there are thousands of Yeerks with each name, than statistically, we should see numbers in the thousands with more regularity, rather than the almost-always-three-digits that we do get. I take this to mean that the Yeerks typically only take 3-digit designations with any given name. Keep in mind that I said "typically."
It's explained in book 6 that the "double digit" designation of the Esplins denotes that they were twins- I've always taken this to mean that they would have been Esplin 946 had their grub grown into a single Yeerk rather than twins. The implication here would be that all 4-digit designations denote something special or unusual about the given Yeerk (though without it being stated we're left with nothing but speculation as to what these unusual things might be).
Based on all of that, I've got my own theory about the Yeerk naming system. There would be multiple given names within each set of grubs (how these are chosen is potentially a whole discussion in itself). Based on the fact that we see numbers between 100 and 999 (I'm counting 9466 as 946), but never less than 100, it seems to me that Yeerks don't use those lower designations for whatever reason. I see no reason to assume that Yeerks are numbered strictly in numerical order- it could be that only two digits (For the moment I'm going to assume it's the second two, since the first always seems to have a nonzero value) count upwards, with the other (first) digit denoting something about the Yeerk. This would limit us to 90-100 Yeerks with any given name (depending on whether the counting of the second two digits starts at 00 or 10- we never see a Yeerk with a 0 as the second digit either). This would make Esplin 9466 the 46th Esplin to be spawned from his set of parents, with the second 6 at the end describing that he's a twin, and the 9 at the beginning showing that he's... something else. Covered in a particularly fragrant slime, perhaps?
Then, of course, there's this- According to Wikipedia, the Yeerk in book 41 had a 6-digit designation (Essak 241275). This lends support to the idea that the Yeerks don't repeat names- as their numbers climb into the multiple billions, this would be harder to maintain, but you would still get the same number of Yeerks from any set of parents. My guess here is that Essak 241 is the given name, and 275 is the Yeerks' numerical designation- his brothers would be Essak 241XXX.
*shrug* Iunno. I'm just spitballin' here.
