1) Can the 4 menu buttons be used in the case that that they are used for emulated Nokia menu navigation and not for gameplay systems?
Yes.
2) May the "whitespace" that the 3310 had bordering the LCD screen be included in the game, assuming that it is not utilized as part of the display area?
Yes, even if you want to include a whole graphic of the phone around the display area that is totally fine. Also if you want to use the mouse to physically click the buttons on the screen that would be okay as well.
3) Are sounds emulating the dull click of pressing the phones buttons allowed?
Anything you want to do, as long as you're trying to emulate the phone is fine.
4) Is accuracy to the phone's operating system necessary in cases where the Nokia's menus and such are represented?
No, but if you want to try to emulate the original phone I would say get as close as you can
Overall I love your idea and I am excited to see it!