We’ve learnt a lot of lessons during the implementation of our Sharepoint project. The number one lesson to take home is this: Sharepoint can’t handle a large number of lists (Document Libraries) in a single site.
We tried a structure with 20000+ libraries in site and, while accessing each of the libaries was fine, it was impossible to enumerate the lists in Sharepoint designer and deploying content type changes took an eternity. Our new structure has 20 libraries each containing 1000 folders (Document sets). None of the previous problems exist.
The sharepoint limitations documentation talks about number of items in a list and various other limitations but never mentions any practical limitation on the number of lists per site… so let this be a warning: a top heavy design will topple over.