Have you ever been to Midway? There is nothing there. The lagoon is too shallow for anything bigger than a destroyer. Large ships have to anchor at sea. No breakwater. No lighthouses. Just a big seaplane hangar built by Pan-American Airways for their trans-Pacific Clippers and the bunch of wooden buildings built by the navy during the war.
TMO and RFB both remade the Islands to be much more historically accurate. Even the sand spit to the left of your second pictures isn't really there.
Sand Island, showing the 'harbor'
Eastern Island, with the airbase
Overall chart showing how hard it is to get into the lagoon
November 1941 photo looking over Eastern Island toward Sand Island