We study the decidability of the topological properties of some objects coming from fractal geometry. We prove that having empty interior is undecidable for the sets defined by two-dimensional graph-directed iterated function systems. These results are obtained by studying a particular class of self-affine sets associated with multi-tape automata. We first establish the undecidability of some language-theoretical properties of such automata, which then translate into undecidability results about their associated self-affine sets.