These holes look like bird activity trying to get at insects under the bark (not necessarily carpenter ants but possibly). It makes sense that the holes showed at the same time, as the insects were likely active and then the birds went after them. I would not advise filling in the holes as you did. It probably won't harm but it won't be a help.

It makes sense that following a storm that damaged and felled trees that carpenter ants would be active on those felled trees. They prefer to make galleries in damp and decaying wood. 

If you are concerned about your oaks having any decay or pest issues that could impact their structure. I would recommend getting the trees inspected by an arborist.

The best way to find such a qualified arborist in your area is to search by location in the link below for an ISA (International Association of Arboriculture) certified arborist.

Resources - ISA Michigan (asm-isa.org)