The Bernoulli numbers are closely related to [alternating permutations][1]. That is to say, permutations like $1524376$ where the numbers alternately go up and down. Specifically, if $A_n$ is the number of such permutations of an $n$ element set, then
$$B_{2n} = (-1)^{n-1} \frac{2n}{4^{2n}-2^{2n}} A_{2n-1}.$$
It's possible you could somehow relate your sums over diagrams to alternating permutations.

  [1]: http://en.wikipedia.org/wiki/Alternating_permutation