If not when will there be a release available that hides the console window? I notice that the timestamp for your reply was 1/2017, I would think that 5 months might be enough time to release a version that hides the window.
This should be fixed in the testing builds. Try installing the third testing build:
https://github.com/goatpig/BitcoinArmory/releases/tag/v0.96.0.3-testing and see if you still see it (I don't see it).