Is there a correct orientation for hurricane clips?
It is always best to consult the manufacturer's manuals and catalogs on this. Simpson Strong-Tie is one brand that is very extensively documented. If you're talking about the diamond plate type, they belong on the outside of the building, and tie the double top plate strongly to the rafter. If you use them on the inside, they only catch the lower truss joist across the join and don't properly attach anything together. 

http://www.strongtie.com/products/connectors/h.asp

Since it's under copyright, I'm not sure if they'd consider a clip to be fair use, so here's a link directly into their PDF Installation notes on installing these things for Rafter and Truss construction. Scroll up or down for other Hurricane Clip and Earthquake ties. 

http://www.strongtie.com/ftp/catalogs/S-INSTALL09.pdf#page=21