Most OSX applications close their window with a command-w shortcut. Any reason this is not supported in the OS X application ?
Please click on the TD icon in the top bar, go to Configuration and you should see a hide/show keyboard shortcut which you can set to any key combination you want.
That is not a solution to the problem unfortunately.
First of all it does not allow me to record that combo. It just returns to "Record Shortcut". Bug or clash with normal window behavior I dont know.
Second, those are global shortcuts (at least it says so). The expected behavior is that it is application local. Otherwise the Todoist window would "show" whenever I use the Command-W combo in another application.
I believe it is as simple as just adding a menu item called "Hide Todoist" with the Command-W shortcut. Would fit nicely in the Window menu.
I have passed this to the developers, we'll look into it and as soon as I hear back from them, I'll let you know. Sorry for the inconvenience.