It depends on your locale/keyboard configuration/physical keyboard layout.
For example, I can perfectly type both characters in my spanish N900. My keyboard is configured as spain/portuguese/french. The '~' is the second keycode in the 'Ñ' key, while '^' is the second keycode in the 'Ç' key.
So, for better answering you:
1) Which country is your N900 from so we can deduce your physical keyboard?
2) What locale have you configured?
is there something wrong whith sys fonts?