From a completely nerd standpoint, shouldn't the nacelles be further away from the ship ?
Well you are seeing it predominantly from the side. Given that these engines are less powerful and that they would show to be further away when seen in other views I think it's okay. Besides they can look closer than they appear because they're attached to a section extending out from the saucer rather than attached to the support hull.
Also what about a destroyer design where the nacelle attaches right to the dorsal? That's even closer to inhabited areas.