The amount of time it takes a scene to capture depends on a few things; how much information is in the scene you are capturing (how many fx chains, algs, etc) and how much scene data has already been saved.
For example, if I have a blank session with no scenes and I create a new scene map, the first scene will capture quickly, but each scene I capture after will take longer because of the previous scenes that were saved. If the scene captures you are doing have many fx chains and algs, this will make the captures take longer.
Let me know if that is the same behavior you are experiencing. We will look into making the scene captures happen quickly when there is previous scene data saved.
I've also added a ticket to have a popup in Emote let you know when a scene is being captured. If this is an issue for you, you can use the front panel to capture scenes and a popup message will show up on the H9k's screen while the scene is capturing.