The cause of this is the plastic from the catch wearing off through use.
With the plastic coating gone, the metal catch rattles against the metal loop.
The fix is simple enough, wrap about 3 layers of black insulation tape
around the bar (marked by a red arrow on the top picture).
Ensure the glass hatch closes properly, if not remove 1 layer of tape at a time until it does.
The rattle should be gone.
If not, try the fix on the lower catches (bottom picture). If this still doesn't fix it check
for anything that may be loose or anything in the storage net. If nothing can be found
check to see if there is any movement in the plastic side windows.
It has also been noted that applying a heavy grease to the lock mechanism can remedy
this problem too as the internals of the lock can buzz with the vibration of the engine..
Also double check the engine cover as it can be tricky to close which may also rattle.