JSON can only represent a subset of the types supported by BSON. To preserve type information, MongoDB adds the extensions to the JSON format - that is the reason the _id value looks like that. When the same JSON is imported into MongoDB (using mongoimport) the _id is once again converted back as ObjectId.
And, I don’t think there is a feature to replace the _id value during the export process. But, you can restrict which fields can be exported.
First, create a view on the source collection. The view definition takes an aggregation pipeline. You can create a new field as you are expecting, id (this has value of ObjectId converted to string) in the pipeline. For example,:
Then, in the command-line do the export using the view, instead of the collection. After the export is complete, the view can be dropped, just like you drop a collection.