I've read multiple times that if you have high chaos, Samuel will shoot a flare to warn the guards after he kcks you out of his boat, but I've finished the game twice in high chaos and he both times just said "I'll let you go this time". So... What's the deal with that?

I think its based on your level of high chaos..Try slaughtering everything that moves next time and you'll be sure to see it!

I had really high chaos on my second playthrough (on purpose) and he was really pissed with me....I was worse than the other three, but he still helped me to save Emily...but he shot in the air to warn them (not a flare, just a gunshot)...not sure if this made the guards aware of me, though...

There are various levels of high chaos. At the bottom of the high chaos, he'll let you go undetected. At the highest of chaos, he might even shoot you.