The Company DOES know that Matt and Mo are raising Molly. Bob said as much when he hired Mohinder. It was couched as a reassurance, but was clearly a threat: "We haven't interfered with that arrangement" {Implied: But we could, if you don't play ball}. However, it's either a) stupid of them not to bug the apartment, since any bad guy worth his salt would, or b) stupid of Matt and Mohinder (nevermind HRG!), not to have thought of it.
It was legitimate for Matt to seek out his father, since he was investigating a series deaths, at least three of which were murders (Patrelli, Linderman, and Hiro's dad), in which his father was his only current lead. But it's absolutely true that a little detective leg work could have gotten him a lot closer to his father before he had to resort to Molly. He's taking the easy way out, and cutting corners, even at the risk of those he loves, which doesn't bode well that we're going to avoid the "evil Matt" of "Five Years Gone".