In my experience with EK ID90 travel, they typically do check your bags from the point of origin to your final destination. If the second leg out of Dubai is tight on seats they will issue you a standby boarding pass at your first point of departure. Once you arrive at Dubai you proceed to the EK Connections counter to get your new boarding pass and they will be aware that you have checked bags.
If you can’t get on the flight out of Dubai, likewise they are aware of your checked bags and they’ll ensure they are not onloaded onto that flight. In this case you can choose to list yourself on the next available flight and you can wait in the transit area without having to collect your checked bags. They will tag them to your flight. Same case if you decide to change destination.
Hope it helps.