I would say the only way they can be really destroyed would be any coins generated during a split in the block chain would be destroyed when one of the chains gets dropped.
No. What can be destroyed, in a way, is an unspent output. Once that output is turned into an input you can't do that again, so in effect it's destroyed.
When you put it this way you are trying to fit the old paradigm to the new. In a way, isn't an unspent output not destroyed but sent back to the whole as deflation. Once that output is turned into an input you can't do that again, so in effect it is of benefit to all the other Bitcoin users.
It seems to me Bitcoin corrects the function of money and has it function more like matter in the real world.