Will readers easily understand the following sentence, or should I express it differently?

What happened, happened, and the past cannot be changed.

Are the commas correctly used? Also, I'm concerned some readers will believe I mistakenly typed the word "happened" twice. Is there a better way to express this, or is it fine?

Looking at a couple of different sources, your phrase is completely acceptable. However, it would create a greater impact on the readers if you divided the above example into two sentences.

"What happened, happened. The past cannot be changed."

The fact that you're using a comma to separate the two "happened"'s, makes it all the more clear to the reader that it was intentional.

Saying, "what happened happened" without the comma feels grammatically wrong in my opinion. In this case, as you said, readers might believe it could have been a typing mistake. Moreover, Grammarly seems to highlight this as well.

You could also (perhaps) cover this idea by using the common idiom, "No use crying over spilt milk".