Update: I have created 4 Rogue Number Holders of different difficulty levels. They will be roaming Heartland during the "After School" topic and, should you manage to gather enough info to discover one of them, a Shadow Duel will ensue: should you win, you will obtain their Number, as well as the major piece of info about the overall plot that comes with it. While I am not going to reveal anything about their identity, location or deck choices at this stage (you'll have to find out for yourselves), I'll have you know that the Numbers they hold are as follows:
Number 30: Acid Golem of Destruction (difficulty level: low)
Number 34: Terror-Byte (difficulty level: low)
Number 12: Crimson Shadow Armor Ninja (difficulty level: medium)
Number 66: Master Key Beetle (difficulty level: high)
Notice that, since a card is only as good as it fits into a deck, the difficulty level doesn't necessarily match how good the Number card is: you might have a hard time to beat a high-difficulty Rogue Number Holder in a grueling duel, only to acquire a Number your deck simply doesn't need, or you might breeze through a duel with a low-level Rogue Number Holder and acquire exactly the Number you needed. Also important to notice that the duel becomes a Shadow Duel, thus involving the not-quite-death enabled clause I explained elsewhere and allowing you to claim the Number, the moment that the Rogue Number Holder actually summons his Number. Therefore, should you beat your opponent before they bring out their Number, you will gain nothing. To spice up things a bit, the non-recurring NPCs (that is, one-shot NPCs that don't appear in the list in the OP) will be more than 4, so that, when you defeat one before they can summon a Number, you will be left guessing: was that really a Rogue Number Holder? Or did you duel the wrong person?
Also it is important to notice that the "After School" topic will have a time limit, which means that the topic ends when time is up, and not when all the Rogue Number Holders are defeated. This means that it might very well be that you won't be able to locate any of the Rogues, or only one of them, or only two. And even if you do locate them, you still need to wait for them to summon their Number and then beat them... At any rate, know that in each "After School" topic there will always be 4 Rogue Number Holders: this means that, should one or more of these I just announced be defeated during the first "After School" topic, I'll create an equal amount to take their place in the second one. Those that are not defeated will simply return in the next "After School" topic, and they'll keep on appearing untill defeated.
Finally, to avoid uverusing the word "info", which would create confusion, as of this moment the critical piece of info about the overall plot, that comes with each Number, shall be known as "Izanami Lore". For example, the piece of info that comes with Utopia is "Izanami Lore #39", while the one that comes with Machu Mech is "Izanami Lore #33". So yeah, during "After School" topics you will be able to acquire two different things: regular info (obtained from NPCs, needed to locate the Rogue Number Holders) and Izanami Lore (you get one for each Number you acquire, you will need these to grasp what is really going on in the plot). Notice that, since Numbers cannot change hands once a player character has obtained them, Izanami Lore cannot be forcefully taken from another player, either: the only way Player A can get to know Payer B's Izanami Lore is to share their own with them (Player A will get to know every Izanami Lore obtained by Player B, but Player B will get to know every Izanami Lore obtained by Player A as well). Sharing such knowledge is actually encouraged, specially in the case of Arcana Number Holders, as you are supposed to cooperate to solve this case (and eventually save the world).
This is all for now.