I should imagine it will be fine as it is what they are designed for - just make sure everything is packed tightly and not going to rattle around too much. First time I flew into Jo'burg with Emirates, there was about 7 peli cases plus other hard cases on the baggage carrousel from a film crew. Just make sure your insurance is up to date, just in case!
As for it reaching its destination, I have never had a problem with Emirates loosing bags (20 flights with them in the past 6 years).