Today after OGM-674, a nested element with no property left is fully nullified. This is a natural approach in most case except if the document is shared between several application and if unknown properties (to OGM) are involved. We could envision offering a option overridable per entity and maybe even per property to up the standard and be extra conservative.
Depending on how MongoDB projection works (today filtered by selectable columns), we could

• load the whole document and not remove non empty elements

• or project the top nested properties (if MongoDB supports that) which would load the whole nested structure. This would load partially the document and would be preferable.

This is probably only useful for MongoDB (I think Neo4J already does that as we load the whole node already).