I think I understand your question. Depending on the OS (Win, Mac, Linux) there will always be a window open when executing, say a PowerShell/Terminal hack with the Ducky. Now there are steps you can take to hide the window/make it less readable, especially on Win. I would suggest white background with yellow text and make the window as small as possible.
This one is for resizing the window size: https://stackoverflow.com/questions/8688846/resize-command-prompt-through-commands
This one is for changing the color's: https://stackoverflow.com/questions/10061961/how-to-change-color-of-new-cmd-window-together-with-a-custom-prompt-created-vi
You can also use the API Move Window to change the position of the window: https://stackoverflow.com/questions/15051649/is-it-possible-to-move-the-command-prompt-to-a-certain-position-on-the-screen
Hopefully that helps,
- wiredbrother