I found out some bugs on Sharpmap branch 1.0:
FeatureDataTable is marked as serializable but it misses the appropriate ctor:
public FeatureDataTable(SerializationInfo info, StreamingContext context) : base(info, context)
FeatureDataSet seems correct, but after deserialization its Tables property is null.
At the end these classes are useless in such scenario, we could anyway replace them with the standard DataTable/DataSet with little effort.