Docs note that:
This utility takes a single file that contains 1 JSON/CSV/TSV string per line and inserts it.
In the structure you are using -assuming the errors on the gist are fixed- you are essentially importing one document with only shops field.
After breaking the data into separate shop docs, import using something like (shops being the collection name, makes more sense than using example):
mongoimport -d test -c shops data.json
and then you can query like:
db.shops.find({"name":x,"categories.type":"shirts"})