From all appearance, SharpDevelop, unlike Visual Studio, uses Reflection
to populate the code completion choices. Visual Studio uses XML documentation files, so Intellisense should continue to work with a protected assembly in its' IDE.
If the options used to protect the DLL include ones that will confuse Reflection, then there probably isn't anything you can do to make it work again. Since Reflection offers such a rich interface for reading assembly metadata, it's often the first step in referse-engineering an assembly, and this is exactly what SmartAssembly is trying to prevent.