There is a lot of factor before a wisteria blooms specially if bonsai. First, it should be mature enough to give flowers...cutting is not recommended if you want it to have flowers soon. you have to take consideration of the condition of the plant too, sometimes some of the variety love to be root bound in the pot before it will flower, it love water and full sun.

If it isn't seeding everywhere and you don't mind doing the heavy pruning, I'd leave it since you like it. You could always build a heavy duty pressure treated structure for it if what you have there already isn't working. Some folks grow them like trees. Look at Claire's and Evonne's in the link below or kt's in this thread: http://forums.gardenweb.com/forums/load/neweng/msg041725213986.html So you really can prune it however you like to please yourself. If it gets out of hand at some point you can remove it, with a large saw and some brushkiller on the remaining roots, though it may need repeat removal to get it completely gone. Here is a link that might be useful: wisteria trees

IME, the flowers are very susceptible to the vagaries of the weather - mine got hammered this year from the windy rainy week, then the ungodly hot week; it was clearly not a combination they liked as they, like yours, fell apart quickly. They aren't long-lasting flowers at best, not like a columbine's flower is, but they usually last longer than they did this year. So, chalk it up to the weather and wait for next year (also known as the Cry of the Gardener).

Can you start at the mother plant and cut everything heading down and sideways? IME you need an air strike to take out wisteria at all, and I doubt that hitting the offspring with RU will affect the mother plant, but if you want to keep the mother plant I can understand your concern. They're a bear to dig up,too. "Sneaky" is not the word that I would use but it does apply.