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!