I know its a late answer, but if you're still looking,
you can use ShowWindow().
you'll need a handle to the current window ( i think GetActiveWindow() ) will work.
then set it to 0 or SW_HIDE
On MSDN search for knowledgebase article Q205158. Here is the summary from it:
SUMMARY
Sometimes, it might be necessary for an application to prevent its main window from appearing on the taskbar. This article describes two ways that this can be accomplished.
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