Late summer is the typical time of year for squirrels to eat pine cones in search of the rich seeds that provide them with nutrition to last the winter. It is also common for squirrels to gather cones and stash them for later use.

Some interesting theories I found for squirrels causing damage to trees include:

1. Squirrels sometimes gnaw on trees during the dry months in search of water.  

2. Gnawing to cope with pain. The idea behind this theory is that pregnant female squirrels late in their term don't eat. So the belief is that they gnaw on bark to cope with the pain.

3. Gnawing in search of food. This theory holds that squirrels are gnawing in search of the inner bark that would satisfy a particular nutritional need.

To prevent squirrels from climbing individual trees try encircling them with a 2 to 3-foot-wide collar of metal 4-6 feet off the ground. To give trees adequate growing space, attach the metal collar using encircling wires held together with springs. The problem with barriers is that sometimes squirrels will jump from tree to tree in the canopies, so you may have to install these barriers on more than one tree.

I do not think that the squirrels will kill your trees, but they may kill individual branches.

Hope this helps.