In this case, I would use the native .dset files then. Importing a .dset file, appending data, and writing back can be surprisingly fast even on rather large datasets. Also with files it's easy to create backup copies, if necessary.
Hot-linking datasets stored in EasyMorph Server is intended exactly for that. The "Import dataset" action can import dataset directly from Server, without creating a local copy. The "Export dataset" action can export directly to Server as well. To get an idea how it can work check out this article: Server Link explained. Note that Server Link is not mandatory for hot-linking. It can be done using regular connectors.
In general, you can think of EasyMorph Server as a dataset/file storage instead of SharePoint. EM Desktop has a number of integrations with EM Server which makes it more convenient to use that any other file storage, such as SharePoint.