The Queen Bee's gimmick is using honey dice to pump up dice values when placed on the specifc tiles on the board.
However, You are correct in that if the honey claims your shield dice, you're going to be out of luck when the big attack happens.
I feel the best you can do is to ensure you have only 2 of each colour type. More dice means more chance of having an unfavourable streak of dice you don't want for a given situation.