The only thing I'd be concerned about with BCX are voids, especially in the interior plies where you can't see/fill them. Also, depending on how you plan to cover the deck, you might need an extra layer of 'glass or fairing compound to get it as smooth as if you used ACX.
The voids would bother more, especially if happened to put a hole (for a seat pedestal screw, for example) through a void. With solid wood (no voids), you could be pretty sure that some sealant in the screw hole would prevent water intrusion. If the screw penetrated a large void, you might not get 100% sealing and there would then be path for water intrusion into the inner plies of the decking. Also, if you're using a thru-bolt and T-nut or similar thru a void, you may not get the same kind of compression as if the wood was solid. (This would be less of a concern if you use a backing plate under seat bases or pedestals.)
Probably be less of a concern to use BCX for stringers, I would think.