Good question. I think, and I don't know shit about bridges and tunnels, but I think the tunnel is probably more expensive. Part of the passage had to be tunnel so they did as much tunnel as they needed and did the rest as a bridge since that was cheaper.
From wikipedia: "The justification for the additional expenditure and complexity related to digging a tunnel for part of the way, rather than raising that section of the bridge, was to avoid interfering with air traffic from the nearby Copenhagen Airport, to provide a clear channel for ships in good weather or bad, and to prevent ice floes from blocking the strait."
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