Actually, a good number of dungeons have a room or two you can completely skip. These usually hold bonus loot, like rupees or pieces of heart.

Heck, that shrine in BotW with the ball maze apparatus. Most people just flip it over and skip the maze. Some even just bomb jump over the gate and skip the apparatus.

Instead, I recommend you just accept that you might work on something the players won't see. Save that stuff for later.