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The entire game is very much based around audio cues, the intended skill Rare want more players to learn is to be able to identify those audio cues and use them to your advantage. Less time needs to be spent watching ladders if you're more experienced and can rely on audio cues. Just like being able to adjust sails to catch wind, you can focus on the horizon or what another ship is doing in combat while using the audio cues to catch wind. Seems very much in line with what Rare appears to deem as "skilled" or "experienced" play.
This is good; silent boarding only worked against crews that were going to let you get aboard anyway, be they new players or experienced crews who were being distracted by something else. There are better ways to offer players more opportunities to get aboard other players' ships than for grabbing the ladder to be silent, anyway.
You can still grab a ladder fairly quietly. If you're in the water and you're lined up with the ladder, stop moving just below the surface and let the ship come to you. It's not the same as a silent board was, but I've found this fairly reliable against a lot of different crew types assuming I haven't been spotted long before I'm at their ship.
Don't worry - our fix here patches a few scenarios where the board SFX wouldn't play, boarding from stationary position and from below the water line should be covered in our fix!