It degrades performance since document stores are basically key-value stores. If you can group these small documents by some logical relationship and you frequently retrieve the documents by this grouping, you might consider "rolling-up" the small documents into larger documents that contain an array of embedded documents.
Rolling up these small documents into logical groupings means that queries to retrieve a group of documents involve sequential reads and fewer random disk accesses. Additionally, rolling up documents and moving common fields to the larger document benefits the creation of an index on these fields. There would be fewer copies of the common fields and there would be fewer associated key entries in the corresponding index. See Indexes for more information on indexes.
However, if you often only need to retrieve a subset of the documents within the group, then rolling up the documents may not provide better performance. Furthermore, if small, separate documents represent the natural model for the data, you should maintain that model.