Well the original music might not have been used so as to avoid having to pay royalties. Trials would already be a fairly expensive episode. As for sound differences that might be down simply to changes in tech from the 1960's to the 1990's.
The only thing that bugs me is they changed the sound effect of the intercom button on Kirk's chair. In the original episode, when he calls McCoy to the bridge, it makes a simple click noise. In the DS9 ep it goes BLALALALALA!
Yes, a tiny change, but...why make it?
Also it kind of bugged me that the episode required them to acknowledge the change in the Klingons' appearance as something that was real in-universe. Before then, it had seemed like the franchise as a whole was following Roddenberry's advice and pretending that Klingons had always had ridges even in TOS, or at least remaining agnostic about it. Well, I don't mind that they acknowledged it so much as the way they handled it. It's hard to believe that the DS9 crew had never heard of ridgeless Klingons before.
Also it kind of bugged me that the episode required them to acknowledge the change in the Klingons' appearance as something that was real in-universe. Before then, it had seemed like the franchise as a whole was following Roddenberry's advice and pretending that Klingons had always had ridges even in TOS, or at least remaining agnostic about it. Well, I don't mind that they acknowledged it so much as the way they handled it. It's hard to believe that the DS9 crew had never heard of ridgeless Klingons before.
I thought it was better to make a joke out of it than to give it the treatment Enterprise did.
DS9 took several asides like this that aren't meant to be taken so seriously. And I love that. "Take Me Out to the Holosuite" comes to mind. "Badda-Bing, Badda-Bang" -- I love the scene where the crew are dressed up walking through the promenade. It's unrealistic even in the fictional universe of DS9, of course, but to me it was a great moment! It's like once in a while the producers would sometimes say "lighten up, people, we're just making a TV show after all! Enjoy it!" I, for one, loved it! 
It was only Bashir and O'Brien who definitely didn't know about the Klingons.
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