If the ability is an always on ability, such as Lady J's Broadsword or Lilith's Sword, both of which give to the flip, you would get those. If the ability is a Trigger, you do not.
Basically with Self Loathing all you get is a damage flip, and Damage flips do NOT activate triggers.
So in Hamelin's case, since its an always on ability, yes the ability, being that its always on, is taken into account and Hamelin would suffer 2 damage from his staff, and he gets a blight counter.