Trunk full of water is likely either the drains in the quarters are clogged (do you hear water sloshing around?) or a leaking seal at the base of the top along the back (this may be called the "rain rail", not really sure). Of course, check the usual suspects like the trunk seal and the taillights as well for possible water entry points.
The wheel bearings on these cars are pretty tough in street use. Sadly, I've replaced lots of control arms due to contact and never a wheel bearing for the same reason. The OE rear wheel bearings went 240K before they got noisy. To check the wheel bearings, jack the car up, grasp the wheel at 12 and 6 and tug. There should be no play. The noise you are describing could well be rear wheel bearings as well. Miata.net is your friend here, but suffice it to say if there is even a hint of rust on the axle splines you're in for a grand old time.
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