So, how come historians have said that Philip and the Pope managed to recover very little wealth from the Templar commanderies, and that the Templar fleet disappeared?

Concerning the wealth, it is known that Philip (The Broke or The Treacherous) of France owed the Templars an absolute fortune, hence he had a very compelling reason to sneakily stab them in the back. This would explain why he found very little wealth, because they had lent it all to him (and various other concerns). All they had were IOUs.