I doubt a vacuum would damage the motherboard, but the high pressure differental will certianly cause any weakness in the seals to give way.

With the dessicant, is there much to worry about?

Another option is to replace the air inside the cube with something without any water in it. Nitrogen and argon are good coices, as they are harmless and since they are heavier than air, you can "pour" them in to insure you get all the air out. Gas supplies can be easily gotten at local welding supply shops.

For some motherboards.. what about puting studs in that can pass through the four mounting holes and then be screwed down to make a good, firm seal against a rubber gasket? No glues needed.