The caller asked about drilling a hole for water drain in the tub where her spare tire resides. Agree that that’s fine so long as she doesn’t puncture something important on the underside. However, there should be a drain plug already there. Drilling should not be necessary, there should already be a hole in the lowest point which was used for exactly that purpose during manufacturing.
I have an 89 Civic hatch, and believe that she may be mistaken about the origins of the water. Likely, it is coming in from the air vents along the sides of her hatch. It goes from there into the side pockets of the rear fenders. From there, when the car moves, it spills out the vents near the hatch floor and goes into the spare tire well.
So the best remedy is to drill, not under the spare, but on each side at the bottom of those hollow fenders.
To check for this,consider:
Does the water come in mostly when the car is standing still? (Car washes, parked in a storm, or snow/ice melting on the hatch will be worst.)
After one of these events, if you pop off the access door to the rear side lights, do you find water in the fender hollow? If so, then that’s your source. (Burning out turn signals too fast is another good clue, as it can slosh that high if it’s really full.)
Until drilling, you can use some surgical tubing to drain those wells. (If you mess up, the water tastes bad, but it’s never made me ill. : P) After drilling, it’s still good to have the tube in the car to break up the bits of trash that can accumulate over those holes. A wet vac with a long hose would be even better, if you have one.
Just for the record, the only place my 22 yr old hatch ever leaks is through those vents.