It is fairly common knowledge now that SharePoint lists and libraries can hold millions of documents, but there is a practical limit of about 2000 documents in any one view or folder. Such limitations are discussed extensively in this Microsoft article [link].
So how do you deal with this when migrating Notes documents to SharePoint?
Notes Migrator for SharePoint customers are certainly subject to the same per-folder limitations. Our tool is very good, however, at assigning folder names dynamically so the problem is mitigated to a significant extent.
For example one, could map the Category field or Territory field in Notes to the Folder name in SharePoint. If these values contain slashes (“/” or “\”) you can use these to generate nested trees of folders and sub-folders. For example map “US/Massachusetts/Newburyport” to a Folder name to get three levels of subfolders.
You can even use formulas to generate folder names dynamically. For example, use the following formula to generate three levels of folders:
Country + "/" + State + "/" + @Uppercase(IndustyCode)
Some customers have gotten pretty creative in creating "randomized" distributions for folder names. In this case, the folder hierarchy is not likely to be a good way to for users navigate documents, as the names are pretty much meaningless to them. As with any huge list of documents, search becomes an important tool for users to search documents here. You can also use tools such as Quest's Web Parts for SharePoint to design much more performant views against large data sources.
Another option is, of course, to split the database into multiple smaller lists and libraries. One good way to do this would be to use a selection formula to extract a portion of the data for a given job run:
Region = "NorthWest"
Breaking huge Notes databases into multiple lists and libraries can also helps with backups. Again, you can use specialized web parts like Web Parts for SharePoint's List View to create a single view of multiple libraries (even across multiple SharePoint sites).