You seem yo be on an "anti-figurative' kick at the moment, 4GS! Language is not always used literally. I'll bet you've said to someone in the past, "I'll kill you!" Did you...'kill him', that is?
Oddly enough, people who are very close to each other often do synchronise bodily motions. For example, women sharing a prison-cell are known to find their menstrual cycles beginning to coincide.
I'm not saying that happens with two sets of heart-beats, but you see the point, I'm sure. In the non-literal sense, the phrase just illustrates a very close relationship where those involved think alike, act alike, believe alike and so on. In other words, "two hearts which beat as one" is a figure of speech, not a factual statement.