Hi, same issue here, but a little more complicated setup: I use a Linux Mint 18 machine, with a German Macintosh keyboard layout, and Chrome as my browser. I have had the same problem on macOS 10.12 also with a German Macintosh keyboard and Chrome. From my testing it seems, that the browser plugin always detects US International keyboard layouts, so if you define your keyboard shortcut to be CTRL+# (which is located on the key directly right of the Ä-key), you'd have to press CTRL+SHIFT+3 instead. One combination that works, because the keys are the same is CTRL+, . Please try to detect the correct keyboard layout from the browser plugin as well, as the main application already does.
Sorry, forgot to mention: Using Enpass 5.3.0