Good question.
Creation of collections is not an issue. Creation of indexes on large-ish / hot data sets might be.
For development, letting mongoose create indexing for you is convenient. In production, you want to think about the potential impact of creating a new index on your data set and when it might be the best time to do so. Ask yourself things like: Is it is a large data set? Am I under heavy load during certain times of the day? On very large data sets, it might even be necessary to add the index using a technique similar to how you perform "rolling upgrades" of your cluster, where you step down a node / take it offline / add the index / bring it back online etc. Just depends how big/hot your dataset is and when you might have less load on it.