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.
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