Hobbes was a loyal member of the Confederation for 15 years, served under Tolwyn on the Concordia, and Tolwyn specifically choose the Victory because, among other things, had an expert on the Kilrathi, Hobbes. He was 100% without a doubt loyal until the "Heart of the Tiger" code was given. There was no reason to doubt him. Maybe they should have checked deeper when he first defected to find programming, but as far as anyone, even Hobbes, knew, he beleived in what he was doing.