The concept of a "bonus level" is in the fact that acquiring the triforce warps you somewhere.

Essentially, you can make a room that cannot be entered in any way except getting a triforce. This room could be a one-time chance to get a piece of heart.

This room could have four buttons If you press the right button, you are insta-warped to an identical room with the buttons pushed and a piece of heart in the center. If you press the wrong button, all of the buttons appear pressed, but there is no piece of heart. A hint in the dungeon could be given as to which button. This method prevents using the lens of truth.

There are even more possibilities.

-Make the player fight an enemy (e.g. Death Darknut) If he dies, he is warped out of the bonus level. If he wins, he gets a piece of heart. The hint would tell players to be at their fighting best.
-Have a shop where you can buy the piece of heart for...500 rupees. The hint would tell players to have a lot of rupees.
-Require a side item that players don't have to have (e.g.Hookshot) to beat the game.