No you will not get water in your trunk the water from the holes will fall down into the "trunk gutter" outside of the trunk seal. I would recommend to just buy a non-spoiler trunk lid from MPS I took my spoiler off and it look great except for the three holes on each side that looke horrible
do a search and u can find the sizes of the holes, then, you can go to home depot and buy some .90 plugs to put in the holes. you can also get some touch up paint to paint the plugs if they dont match
With a light, I could see my trunk mat through the front 2 holes and the 2 rear holes are hidden behind 2 rubber covers - so I'd have to think that you'd get water through the front 2. That was before I installed the "R" wing and filled in the original factory holes.
Actually, it will depend on what spoiler you have. If you have the factory wrap around wing, 99+ style then you will not get water in the holes. If you have the factory pedistool (sp) wing then the mounting holes are on the inside of the seal and water will come into your trunk.
Since yours is an 02, I believe it comes with the latter of the two and will leak water. The best way to check however is to just take it off and see if you see trunk or not, (assuming you have nothing covering the holes from the underside). If you do see trunk, get some silicone and bead it around the plugs until you can buy a new trunk or have the holes properly filled.