If you want to limit the serialization of items under the Navigation item to the...

To limit the serialization of items under the Navigation item to the item itself and those one step below, you should add the scope property to the includes. The scope property specifies the range of content items to include or exclude from serialization. The possible values are: ItemOnly, ItemAndDescendants, ItemAndAncestors, and ItemAndSiblings. In this case, the scope should be set to ItemAndDescendants, which means the include will serialize the Navigation item and all its direct children. For example, if the Navigation item has the path /sitecore/content/home/navigation, you can add an include like this:

“items”: { “includes”: [ { “name”: “navigation”, “path”: “/sitecore/content/home/navigation”, “scope”: “ItemAndDescendants” } ] }

References:

Sitecore Content Serialization structural overview

Sitecore Content Serialization configuration reference