There is space hidden away between the cabin and the boot that has room for small amps:

"Tunnels into trunk
There are two tunnels that run from the trunk into the cabin. Both can be reached from the trunk; the right one by removing the spare tire, and the left one by removing the panels that cover the gas tank fill tube. From the cabin, first lift away the carpet (held by many plastic pins) and then remove the large metal sheet held in place by countless screws. In order to remove this piece, it can be helpful to remove the plastic piece covering the seat belt towers, otherwise it is necessary to bend the metal panel a little bit in order to ease it out.
These tunnels provide an easy way to run wires between the trunk and cabin. In addition, the space can be used for installing various components such as a crossovers or amplifiers (there might not be enough ventilation for higher power amps that generate more heat though)."

This is from one of the articles at:

Miata.net

Some people have gone to the trouble of fitting sub woofers into the rear shelf, using the two tunnels and boot as a resonator.

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