In my next game session I'm going to be running the parrot island section of There is no Honour. I have a pretty canny group of PCs and I doubt they'll be stupid enough to fall for Vanthus's trap. I expect they'll leave a guard, and if they do go down into the pit I imagine that they'll realize it was intended to be a trap when they encounter the zombies, which will result in them fleeing the tunnels.
If they don't recover the letter, what other ways could they get the information they need to advance the story?
Hmmm...that's an interesting problem. Perhaps a friend or lover of Penkus could pay them to go down to Parrot Island and recover his body? That would get them to find the letter.
How do you think they'd react to the undead walking around in city limits? They wouldn't clear out the tunnels anyway? Would they go to the city watch? If they notify the city watch, perhaps the watch could ask them to clear it out for them (they're undermanned) or after the watch clears it out (or hires priests to clear it out), they bring the note to Lavinia, to let her know that they're looking for her brother. She shares the note with the PCs then.
-Jamie
Another idea, maybe Penkus didn't die quite so soon after writing his note. With his last ounce(s) of strength, he finds the underwater escape, and his drowned and diseased body washes ashore in Cudgel district, the note still in his pocket. Then the watch notifies Lavinia, and she brings the PCs into it.
-Jamie