Well, you do get to see all the dark sides of Amnish society(slavery, corruption, etc).

Then there is the 'dark side' of you; the taint,,,

For a moment I thought we were talking Wheel of time here;)
But no, I don't think they mean the taint with 'shadows of Amn'.
If they would, Shadows of Bhaal would have been a more logical choice.

It could mean the shadow thieves, because they play a big part in it even right from the begining when they attack Irenicus' dungeon?

"For a moment I thought we were talking Wheel of time here;)"
hahaha very funny. embrace saidar! lose yourself in the river of molten fire! blah blah blah; create a fire-heron-marked-blade. Become the dragon reborn,. yeah i've read the seris.