Nanodots may not always have crystalline structure, but their amorphicity is very low due to their small size (nanometer). It's like an imperfect crystal; one can easily recognize that locally, is perfect crystal. In addition, the properties of the nano-structures are more similar to crystalline structures than to amorphous structures.
However, if it’s just a question of terminology, why not to use the term of nanostructures for nano-dots, and leave nano-crystals for sure crystalline nano-dots (ie: proved with DRX characterization).