I'm a bit confused. If your input scanning rate is slow, you can sample an input, transmit the appropriate data, and then wait an eternity before you scan the next input and transmit the next data, right? The time required to transmit the data is tiny compared to your data rate, right? Those decoders have a latched output, so I'm not sure why you're worried about flickering. It seems to me a single encoder/decoder should work.
Maybe a block diagram will help.