Personal Tutor #1 - Yes and No
Towards avoiding the issues we had in the zeroth Personal Tutor, let's hash out the “why” first:
First of all, if Neurotoxin animates Inkmoth Nexus, it WILL have infect. This follows from timestamps in layer 6: Melira will remove Infect abilities from all creatures first, and then Inkmoth's ability gives it infect, circumventing the loss, if you will.
Next, Inkmoth WILL “deal damage”, but it won't have any effect. This is due to the technicalities of how damage works, which are detailed in 119.4. A quick overview:
1) Damage is “dealt”, with any prevention or replacement effects directly appended to that “dealing of damage” taken into account. Melira doesn't count here, since she doesn't modify damage: she modifies counters being placed.
2) The results of the damage are processed. In this case, the results (if Inkmoth blocks Melira) will be: “2 points of damage are marked on Inkmoth by Melira” and “One -1/-1 counter is placed on Melira by Inkmoth”.
3) The results are applied, modified by whichever replacement effects may apply. THIS is where Melira comes in: since she cannot have counters placed on her, the “One -1/-1 counter is placed on Melira by Inkmoth” result “fizzles”, and 2 damage is marked on Inkmoth.
So, with that out of the way, we still have to determine what to tell Neurotoxin here. Since the biggest thing we're avoiding is guiding his play based on our answer, staying vague until the actual scenario comes up is probably for the best. I'm not convinced this is the best, but perhaps just dodging the question is the best approach here? “It's complicated. I'm happy to answer your question, but I can't give you any information that will affect your decisions in the game. If the scenario does actually come up, I'm glad to walk you through the interactions, however.”