With Dynamics CRM 2016 with server-side SharePoint integration, the documents list in CRM does not display subfolders. For example, say you have 100 documents in a SharePoint documents folder associated with an opportunity. With the old SharePoint List Component, users would commonly create subfolders in CRM SharePoint document folders to organize documents by type.
With this in mind, I created a Microsoft Connect product suggestion that server-side SharePoint integration should display subfolders (you can vote for it here).
Jukka Niiranen quickly pointed out that while the document list does not show the subfolder icons, the documents in the subfolders are still displayed. This design is most likely due to the product direction to show files from multiple sources within a unified grid, including SharePoint, OneDrive for Business, and Office Groups. Plus, it is displaying them not only in browser, but they are also now available in mobile.
And while you cannot see the folder icons, the path of the document is displayed, so you can sort and filter the list based on folder location.