How to interpret "Mr. Peter had two sons"?

The only thing the sentence states is that the relationship occurred in the past. This is because the past tense is used. If the relationship still exists then it would be normal to use the present, unless we are specifically talking about a past time.

The relationship might be in the past because Mr Peter is dead, or one or more of the sons is dead, or because Mr Peter subsequently had a third son, or because one of the sons became a daughter, or any number of conditions that mean "Mr Peter has two sons" is no longer true.

An example of talking specifically about the past might be:

In 2010 John had one daughter. Peter had two sons.

This state's only the number of sons Peter had in 2010, and nothing about whether it is still the case.

We can say that Peter had a wife and two sons if he actually did have those relationships in the past. If Peter is dead it would be normal to use the past, and to use the present if all are still alive.

If two of Peter's five siblings are dead, it is normal to use the past when talking about the relationship to them.

Peter had five siblings. Two are dead and three are still alive.

Peter has three siblings. He used to have five but two are dead.

Frank Smith, Jack Jones, and Ralph Peter arrived at the father-son banquet. Mr Smith and Mr Jones each had one son with them. Mr Peter had two sons.