Answering the question myself: Yes, fc layers are currently not supported, and it is written at the top of the Deep Network Quantizer description: "Use the Deep Network Quantizer app to reduce the memory requirement of a deep neural network by quantizing weights, biases, and activations of convolution layers to 8-bit scaled integer data types."
But! You can replace fc layer with a conv layer with filters' size equal to prev layer output dims, so they will only be applied once.