< That's a link.
I'd still clean out and prime the holes.

-- Chuck

 

Just checked, seem to be drilled with 3/8" drill bit.

I'm considering these: and using the 9.53 ~ 3/8.
They look like they are meant to be used as a grommet for wiring, but they should work.
The others may come in handy in the future

 

The Honda del Sol had one drain hole (Mainly for condesend water) at the bottom of the trunk pan, from the factory.
The S2000 surprisingly not. Allways puzzles me...

 

I never knew what the two OEM hard plastic plugs at the bottom of our trunk pan were for.

Mine did not appear to have holes for drainage, so one day early in my ownership, I took a flathead and gave it a light love tap and it made a slight hole in the plug. I always wondered if they were supposed to be stamped out and have holes for drainage straight from the manufacturer (probably not), but alas it works.

P.S. Soviet does indeed refer to them as drain plugs, p/n 91611-SM4-003 shown on his DIY here https://www.s2ki.com/forums/s2000-un.../#&gid=1&pid=6

 

The del Sol also had the bigger rubber plugs from the factory, coated with unerbody protection. But it also had a tiny hole for water drainage.
This tiny drain hole was coverd from road dirt, it was hidden inside the reinforced sheet metall part for the tow hook. Clever solution!
I discoverd the drain hole accidently, as i managed to pour 5 liters of destilled water into the trunk of my del Sol and found to my big surprise the water draining hole. Al i had to do was to dry the carpet and wipe out the trunk...
It also helps to prevent rust, because it drains condensed water that accumulates at the bottom of the trunk. All in all, it was a good and clever feature!

Thats why i am so puzzled that the S2000 dont have this feature.

The two big holes that are coverd with the plastic plugs are usually drain holes to let primer flow out of the body in the factory, to my knowledge. Every car has this. Most car bodys get a bath in a gigantic bath tube with primer in the factory before painting. The side sills of the S2000 also have a myriad of them. Handy acces for rust proofing.