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Did Palpatine know (via the force) that the Yuzahn Vong were coming? And was he preparing the Imperial military machine to meet them? Or had he no idea?

See this thread. Nothing definitive, by any means, but there was a very good chance that Palpatine could have at least foreseen the major events of NJO (such as the fall of Coruscant) even if he couldn't have seen the Yuuzhan Vong directly.

There are some SW-fansites, that claim, that Palpatine used the threat of extragalactic invaders as justification to built up the imperial forces - but until now i have seen nothing official that supports those claims.