What I don't get about "there's a lot I can't tell you" is that he is obviously referring to the Roth deal in Cuba because earlier that day he asked Tom to leave the room before he and Johnny Ola talked. Yet when Michael and Fredo escaped Cuba, Tom seemed to know everything about it, right down to what happened to Roth. When did he learn of all this?
DT, I think that Mike was referring to many things that he withheld from Tom and he said it as a way of mollifying Tom at that particular moment. It was a particular moment because Tom was the only one that Mike could absolutely trust in those circumstances. Remember, Mike tells him that he keeps info from him because he loves and respects him. Of course, that's a lie. Mike never forgave Tom for not protecting his father and his brother. That is really evident in GFII near the end when Mike asks Tom is he is going to stay. Even in GFIII Mike is still referring to Tom just as a lawyer. So, as he does with so many people, Mike is manipulating Tom.
As far as Tom knowing about Roth, etc., that was probably info that Tom, being in the position he was in the underworld, came to know about thorugh his sources.