Squarespace have reengineered the Search Block and there's a way to put it in the header/top level navigation using the dedicated search page yourwebsite.com/search and add a link page with that search address to your top level navigation.
Credit to @SquarespaceGuru for this tip, check out write up which explains it better and subscribe to his newsletter, Squarespace Updates the Search Block and Squarespace: Using the Search Block.
Note: If you have an old Search Block you may need to delete it and add a new Search Block to get it to work.