Many areas in smash run for the 3ds are difficult to reach, but not impossible. Because of the fact that getting more stat boosts makes it more possible, I wouldn't consider them "secret areas," but I will briefly explain the different scenarios possible:
-The battlefield like arena has two possible endings. It can simply stop near more platforms, or you can be given a time limit to defeat enemies. Both usually reward many bonuses as when there is no battle, there is usually a chest.
-There are many areas only accessible through falling, through using the cannon barrels, or having a multi-jumper like Kirby or Jigglypuff.
-Sometimes an event will trigger a room's appearance that literally isn't on the map. These are the closest things to "secret areas."
Otherwise, anything is possible with the right fighter.