To me the problem is that a warrant canary could theoretically be completely legal, but the government could bankrupt you with legal fees before you even got to court.
That is probably what WhisperSystem's attorneys have advised them.
This makes more sense—being held in contempt of court is not in itself a ruling (i.e. canary warrants are not in themselves illegal, but disobeying the court is), and is extremely difficult to fight.
That is probably what WhisperSystem's attorneys have advised them.