Beyond calling Blizzard to buff Nydus HP and increase unload speed, a work-around exists -- Double Nydus Worm!
Building two Wurms at the same spot creates a location at which units can be unloaded at double their normal rate, making Zergling-heavy armies able to use the exits more effectively. I'm not 100% sure, but I believe this also doubles the rate loading into the wurms, provided you micro effectively.
With two Nydus Networks, two Nydus Wurms can be built simultaneously. Building them at different locations simultaneously increases the chance of sneaking one in, just as two simultaneous drops are often much more effective than a single one. And of course, two Wurms at the same location can be built in half the time with two Networks.
Of course, 150/200 for an extra Network is not a light investment, and this is probably only practical mid-late game, or perhaps in some other ultra-specific or cheesy scenario. Additionally, two Wurms in one location is twice the investment, and twice the loss when destroyed. Perhaps a few Spines and Spores at a double-Wurm exit would protect the area long enough for you to unload (and at twice the speed!).
Just some food for thought. I haven't actually tried this in a serious game, but it's an idea.
P.S. - some findings; If units are loaded in a Nydus, and all of the Networks are destroyed, the functioning Wurms can still load/unload units, the only issue is that no more Wurms can be made. If all Networks AND Wurms are destroyed, the Nydus'd units die; Building another Nydus Network will not bring them back.
tl;dr - Two Nydus Worms at the same spot = double unload rate. Two Nydus Networks = build 2 Wurms at once.