I would say that there are two ways to explain the discrepancy between Jefferson’s words in the Declaration about the equality of men and his enslavement of the children the Sally Hemings bore him. First, we can imagine that Jefferson was simply a hypocrite. It is not at all uncommon for people to espouse a given moral or philosophical position and then to abandon that position when it is convenient for them. In this case, it was convenient for Jefferson to espouse the principle of equality in public. By doing so, he was able to advance the case for American independence from Britain. However, it was convenient to abandon that principle in his private life. By abandoning the principle, he could keep himself financial solvent (for the most part) through his plantation. By abandoning the principle, he could satisfy his sexual desires. It is not hard to believe that this would be possible for most people as we human beings are extremely fallible when it comes to having to give up convenience in order to honor principles.
Second, we can imagine that Jefferson truly did not see people of African descent as “men.” There have been many instances in history where one group of people saw other groups of people as less than fully human. It is possible to argue that Jefferson was such a person. If whites believed that blacks were truly less than human, there would be no problem with excluding them from the ranks of those who were born equal. White women were also excluded from those ranks, in part because men thought them to be inherently inferior. If it was possible for white men to think that white women were not born equal to them, it was certainly possible for them to think that black men were also inferior. I would argue that one or both of these factors explain the discrepancy mentioned in this question.
As to the second part of your question, I believe that this showed that Americans understood the fundamental hypocrisy of their support of slavery. Jefferson included the passage, in my view, as a way to make the King of England, and the British government, look bad. He was trying to think of every possible crime with which to charge the King and slavery was one that seemed convenient. I would argue that Congress deleted the passage because they understood that American society was implicated in the slave trade just as much as Britain. They realized that England could not bring slaves over to the colonies and force colonists to buy them. They understood very well that they supported slavery and were just as responsible as the King for it. Therefore, they felt that this would be an ineffective attack on England that could actually rebound and work against the cause of American independence. This tells us, then, that society viewed slavery as abhorrent. They knew that accusing the King of promoting slavery would tar his reputation and they realized that it would hurt them to have people focus on their support of the same institution.