I couldn't possibly care less about the sound effects being 'old school' and I don't worry about whether sound effects are 'canon'.
I think the sound effect should fit with what's on the screen - regardless of 'canon'.
You're right, but if there was a way to include the old sound effects (or modern facsimiles of them) in a manner that doesn't seem cheesey, then I say 'why not?'
I think the boatswain's whistle could easily be used for the ship's intercom. The one in TOS was "electronic sounding" enough to fit a 2009 film.
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