Unless I'm blind, I have not seen a hotkey, nor the option to set a hotkey for the Merge Chests button.
Could this be implemented in a future release? Practically every mod I can think of in the game has a hotkey, as well as the ability to set one.
Curiously, there is only the option to set a hotkey for rotating a blueprint with wide-chests in it, which seems a bit clunky since there already are rotate and flip buttons that could be mod-natively made to do the same.