It seems as though this issue has been solved by VS Code implementing a special shortcut for sending text to the serial port.
See the discussion here: Feature request: Enable input for serial monitor · Issue #463 · microsoft/vscode-arduino · GitHub
SOLUTION: As long as you have the Arduino Extension installed (which I presume you do) then just open the Command Palette (command+shift+p on a mac) and type "Arduino: Send Text To Serial Port". This then turns the Command Palette text box into an input text box so that anything you type into it is then sent to the serial port once you hit "enter".
I'll attach a screenshot from the answer in the thread linked above (hope that's ok).
Hopefully I understood your problem correctly and this helps!
