I think it has to do with not being in normal space, but in subspace. A ship would just travel through a planet or whatever occupying the same point in normal space. At least that's how it works in the Stargate universe.
At higher warp speeds, what keeps a starship from flying through a planet or a sun, is it possible to control your flight path at such high speeds. And what would happen if your starship did have a close encounter with such an object??
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