You could tie the hood prop down and see if it stops the noise, The hood
latch mechanism is known for squeaking when it has not been greased, so
I guess it could rattle as well.

Here is a page on tracking down noises on the miata. There is one
section specifically on hood noises.

http://miata.net/garage/noises.html

You might also want to check things like your exhaust manifold & heat
shield bolts that may be loose and expand as they heat up.
Same with radiator mounting bolts, etc., almost anything can start
making noises in there and they can be very hard to locate, especially
when the noise goes away as the car heats up.

Good luck,

Pat

Everything rattles in my car when it's cold.  I think it's par for the
course.