Yep, on either side near te edge. I left mine out as well..... and then took a 2" holesaw and made the holes bigger. Just to make it a little bit louder. :D

Interesting........but I've never farted before. :D :D

So on plane, there wouldn't be any water in the box?

This is really going to sound stupid, but its got wet exhaust, right? So the box is filled with the water thats coming out of the exhaust, not from just being in the water and filling up.. So opening the plugs wouldn't completely drain it, it would just keep the water from getting too "deep" inside the box and less sound absorption..

Correct. Instead of drilling larger holes in the bottom of the platform, I cut out the baffles which are about 4"-5" inside the exhaust tips. I used a sawzall with a long blade and it took all of about 5 minutes. A little louder, but nowhere near thru-hull.

When you're on plane, the faster you run the higher the exhaust pressure. This effectively "blows" the accumulated water out of the platform. The exhaust still has to force itself under the baffles but since the baffles are no longer submerged, you get less back pressure and louder exhaust. It really is an ingenious design that quiets the engines around the docks but results in no appreciable loss of exhaust flow at speed. It was (is) a patented Formula design. Very cool!

The later models, Fastechs, initially used a somewhat modified Silent Thunder design. Essentially the same except that the "box" was really just a panel under the platform that rattled and cracked. It was just too wimpy. The earlier models with the full ST platform were much better but still susceptible to exhaust leakage and rot of the embedded wood in the platform.

http://img818.imageshack.us/img818/3028/alsidjfo9.jpg

Is this what you're talking about? It looks like the plugs have already been pulled out of mine.

Yep. A regular transom type rubber plug (for a smaller boat) can be inserted in there if you want to try it.

Silent thunder
 

is when you eat a pot of fresh baked beans then you go to bed and you pass gas vary quietly and pull the covers over the old ladys head...

Just run the Silent Thunder as is. Leave it alone.
The design works great with no real issues.
Opening up the baffles makes it a little louder, but you get ZERO prrformance gains. Unless you are running BIG power through it, the ST can handle everything you can dish out.
The ST is cooled by wet exhaust and does not have much water in it once on plane. If you listen real close you can hear the difference when the water that filled the ST at idle, drains and starts blowing out the back unrestricted.
I cut holes in an older ST on a 272 and it made the rubber flappers vibrate and sound like crap at idle around the docks. The extra exhaust flow really screwed it up.

LMFAO! Thats one way of putting it!