Hey,
I have the same problem.
I tried it with the "keyboard setting", not just for Skitch, even for Skitch Helper, and the hotkey shows correctly in the menu bar, but it still reacts to cmd + shift + 5, instead of the custom one.
It would be very nice, if you could add the hotkey mapping functionality (I don't think that this is hard to implement ).
Currently I can't open the Helper because of a conflict.
Kind regards