Confusion with cosine similarity
Of course cosine similarity is not proper for searching a specific features in documents! To do this, you can exactly using dot product, as it will ignore zero features in query vector from documents. 

Cosine similarity, in the current context, can be used to finding similarity between two documents. So, all features can be important to finding similarity. It means, if there is not a feature in query vector, but there is in  a document, or vice versa, these two are 100 percent similar. Hence, it makes sense.