What is the possibility of minnows escaping my minnow trap through natural means?

If the trap isn't broken, with an opening they can get out of, the fish can't get out by themselves. So most likely someone else is raiding your trap.

Time to get paranoid!

If it were me, I'd take a good look at my trap(s) and check if there were any defects. If I found none that would explain my missing bait...go to plan 2.

PLAN 2: Start looking at the ones close to you who know where you set up shop. A friend of a friend is no friend of yours type deal. It could be some one spilled the milk and your spot is compromised.

Then again, it could be some one you know and is just playing you.

Now, for the not so paranoid part:

It could be that you have been baiting this spot for so long with the same trap (s) that the fish got wise. Fish aren't as dumb as ya think! They enter to feed in the beginning and get stuck. It takes only one to find it's way out to teach the others. Over time that just means a free meal in the safety of your trap leaving you with an empty trap and obese bait fish. Change up the trap and see if that's all it is.

Before you get twisted, look into the traps themselves before considering your friends or who ever. There's always an explanation to every situation. Keep your wits about you, investigate and find out the correct answer before jumping to conclusions. It's only bait. ; ) ~Good luck catchin'.