Sorry for the late response, but I was away.
The centrality code in graph-tool comes straight from BGL, so details
about its implementation should be looked there. I believe, however,
that it should work with multigraphs out of the box, one way or
another. I'm not sure though if paths going throw parallel edges count
as two paths, or only one. I have to take a look at the code in the BGL
to find out. I'm a bit short on time at the moment, but if I find the
answer before you do, I'll post it here.
Cheers,
Tiago