Deric,
It's not that it won't work, it's that it's not the right application. using silicone to adhere acrylic to glass isn't going to work the way it's intended to. for the simple fact that they both expand and contract to temperature fluctuation differently. Also silicone doesn't stick to acrylic very long. give it a few months and it won't have a water tight seal anymore. So in essence all your doing is using the silicone to form a slot for the baffles to sit in.
With that being said, people do it all the time for 2 reasons. One: Who really cares if the baffles are water tight? as long as your glass tank hods the water in you can have some seepage through the baffles. And second: Convenience, almost everybody can cut acrylic to size, not everyone can cut glass (who wants to pay a glass shop to cut baffles?).
Hopefully this clears things up for you. If your goal is to achieve a water tight seal use glass baffles and silicone them in place. To use acrylic will work it just isn't ideal.