Why did the Baudelaires not tell Ishmael about the danger?

[Foxy]

I think they were worried that if they shared part of the truth, they were going to have to tell a lot more truths that maybe didn't shine them in the most positive light. And they didn't want to drown or starve to death on the coastal shelf, although I daresay they are resourceful enough they would have figured something out.

If they told Ishmael they knew Count Olaf had the medusoid mycelium, or at this point, just that it was somewhere on the coastal shelf, he would have wanted to know how it got there, where it came from, and how they knew about it. And if they said it broke off the boat during the storm, it came from the Hotel Denouement and before that the Gorgonian Grotto, and they knew about it because it had infected Sunny and they had been walking through it while looking for the sugar bowl, Ishmael would have already known they were "trouble," not to mention all the other questions these stories would lead to.

[Optimism is my Phil-osophy]

Unfortunately I think the best answer is: humans make mistakes.

[Dante]

I think there's also a reasonable argument that they didn't think Count Olaf was likely to unleash the Medusoid Mycelium, since it would be impossible for him to do so without infecting himself as well; Klaus asserts this on page 12. Once it appears that there's an actual danger of this happening, the Baudelaires do in fact attempt to issue a warning, on page 254.

[Foxy]

It is probably likely they didn't think Count Olaf would unleash the MM, but it was kind of naive of them to think so. Count Olaf was a madman. He was capable of all sorts of heinous crimes. And he didn't really have anything to live for. He has no family, no friends, can't go back to his house, etc...