The "Maximal Duration" for organic layout (and all other layout algorithms) is a "preferred maximal duration". yEd's layout algorithms usually have a way of calculating low(er)-quality and high-quality arrangements. The algorithms have logic to switch from high-quality to low(er)-quality when approaching or exceeding the specified duration. However, for lots of elements, even calculating low-quality arrangements may exceed specified durations. Given the number of elements in your graph, it is very likely that calculating even a low-quality solution will exceed 30 seconds. Moreover, aside from the number of elements, the structure of the graph has a major impact on runtime as well. And since the number of edges in your graph is roughly eight times higher than the number of nodes, your graph's structure is probably not "good" either.
That said, I cannot rule out that you might have triggered a problem in the algorithm. However, to be sure I would actually need your graph (in GraphML format) for testing.
Finally, the only reliable fix is actually working with less elements. The main purpose of layout algorithms is arranging graphs in a way that is concise and clear to human beings. As a result, most layout algorithms are meant for small to mid-sized graphs, i.e. graphs with up to a few hundred elements only. Because not matter how good the layout of a graph, human beings cannot understand structures with 40000 elements. And while organic layout actually is the best-suited algorithm for larger structures, 40000 elements are still a lot.
