Really? Please name a single congressional chaplain who was a deist.
Also, why would a deist trust in God? What point would there be in trusting in a deity who is uninterested in the affiars of men?
The argument that congressional chaplains are constitutional is not that they have to be Deists but that it has been an old tradition (predating the Constitution by 16 years IIANM) and that their function is mainly ceremonial.
Even Madison (as well as other founding fathers) recognized that this practice wasn't kosher according to the constitution but he concluded that is was de minimis and thus he decided not to rock the boat and give it a pass since there were more important matters to be addressed at that time.
Of course if congressional chaplains didn't exists and someone wanted to introduce them today then this would most likely be ruled to be unconstitutional but since it's a long-running tradition it's deemed OK.