Vito tells Tom:

1. That he never thought he was a bad consigliere, but that Santino was a bad Don.

2. That he (Tom) has all his confidence as does Michael.

3. That there are reasons Tom cannot be a part of what's going to happen (IMHO the reasons are one reason...Michael doesn't want him around).

So given all that I believe Vito trusted Tom even if he harbored unspoken doubts about whether he was an efective wartime consigliere.

Keep in mind when Tom is first introduced Michael tells Kay he is going to be consigliere, and he goes out of his way to mention that Tom is not a Sicilian. This shows Michael's less than high regard for Tom even before he gets into the family business.