The highest frequencies might be affected by the sealer and reflect a bit more, but it depends on the grain and the cut of the wood. It's going to be a minimal effect and either way you are likely to need some more serious sound absorbers like sonex or the like to tame the first reflections in the room and probably the rear of the room (if it's wood too--bookshelfs with lots of books in the back is a nice aesthetic way to help that). I would use the sealer to keep the wood looking good. I'm not sure I'm picturing how the joists run correctly, but you may be able to experiment with absorbers in the corners of the joists if you have reflection problems there. It sounds like the joists will act as a nice diffuser to some degree.
Room acoustics - finished or unfinished wood
I have a 25 ft by 16 ft listening room with 9 1/2 foot ceilings, with exposed spruce joists running parallel to the short wall...7.5 inches deep and about 14" between each pair. My painter, also an audiophile, recommends following a coat of stain with a coat of polyurethane sealer. The question is basic, will unsealed wood better attenuate the high frequencies than wood sealed with polyurethane (flat)? The room probably needs some high frequency attenuation, given wood floors, etc.
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