At the no sound in space crowd.. Yeah, that's like pointing out that fire is hot. It's also totally missing the fact that sound, for humans, and many animals, is a really helpful and important part of situational awareness. It's really easy to imagine (and I'd say very likely) for a futuristic space ship to employ simulated sounds to aid the crew in knowing wtf is going on. Think of it as augmented reality, or like an extra fancy audio version of the HUD you see on military aircraft.
Also, the singing crystal, being some kind of extra-dimensional door knocker to summon crystal alien lifeforms, could well be emitting something more akin to a psionic scream. Covering your ears to try and block that out would be a normal reaction, even if it does nothing, since the sound in in your head. Or maybe the ships augmented reality audio system has a horrible screech programmed into it when a singing crystal rift opens up, just to make sure everyone is totally aware something bad just happened. /shrug.