Here are the most common leaks for a Gen 3 Integra. Not sure about your model but maybe this will point you in the right direction:
Water cominging from moonroof:Clogged drain tube(s) are just one of the possibilities. Also check rubber gaskets around the moonroof. This type of leak should show up in the headliner.
Water in the driver's or front passenger footwell:
This could indicate that the problem is either where the drain hose goes into the rubber valve or a problem with the rubber valve itself. A leak around the windshield could also be the culprit.
Water in the rear seat footwells:
This is probably water that has sloshed over the gas tank from the trunk and would indicate standing water in the trunk. If the water is in this area only I would check the seal around the quarter windows.
Trunk/Hatch Area:
Driver's Side
1. Bottom of antenna mast to hose.
2. Antenna mast hose to y connection on 'rubber' valve.
3. Moon roof hose to 'rubber' valve.
4. Blockage in 'rubber' valve.
Passenger Side
1. Moon roof hose to 'rubber' valve.
2. Blockage in 'rubber' valve.
Other possible points of entry for water; where antenna passes through the body, rear taillight gaskets failure, rubber trim around the hatch itself and the overflow drain from the gas filler.
If you are not sure where the problem is, remove the interior at the "suspect" location so you can see the possible leak points. Have friend spray the car with a hose while you sit inside and look for the leak.
Have you actually checked the hoses for blockage? This is easy. With the moonroof open, CAREFULLY pour a cup of water into each of the four drain holes in the moonroof. If water comes out on the ground behind the respective front or rear wheel that hose is not blocked.
If one is blocked, I would try LOW PRESSURE air to try and clear the blockage. If this doesn't work I would then clear the rubber valve where the drain hose exits the car. This has a design flaw that allows debris to buld up until it blocks the drain. This causes the water to leak from where the hose slides into the valve. HINT: Reassemble with silicon.
Hope this helps