Does God judge sins that are done only covertly?
Yes. God's judgment is according to truth against those who commit such things, even if only covertly. No one who judges others while doing the same things, outwardly or inwardly, will escape that judgment; even thinking a sin in the heart makes one just as guilty.
Les explains that this passage exposes the self-righteous person who judges another. A person may not commit a sin overtly, but the same sin can be present covertly or in the thinking processes. God's judgment is according to truth against those who commit such things, even if only covertly. The one who judges another and does the same will not escape God's judgment. Les illustrates that a good person who would never enter a homosexual relationship can still be mentally just as guilty. Jesus took the commandment against adultery so far that thinking it in the heart makes a person just as guilty as the one who does it. That is hard to comprehend, but it is what the book says and what Jesus said.
But we are sure that the judgment of God is according to truth against them which commit such things.