Question
I have a +100 yr old oak with large holes that fill with dirt and leaves.  Should I seal these holes?

Answer
There is no need to fill the holes. A decay fungi has entered the woody dead cells of the trunk and over time has decayed the wood. The living cells of a tree are just under the bark and are not damaged by decay fungi. To fill the hole would be similar to a dentist and a decaying tooth, First you would have to remove all the decaying material down to solid wood and then treat the wood with a fungicide and then fill the hole. The decay goes deep into the trunk and it would be impossible to excavate all the bad wood and really not needed. A tree can live a great life after it becomes hollow from decay. I would  not do anything but maybe fertilize the tree with 10-10-10 fertilizer at the rate of 1 lb of fertilizer per inch of trunk diameter scattered around the tree and watered in good. Apply the fertilizer just before a rain storm and  you will nor have to water. This will increase the overall health of the tree and help the tree to fight off or slow the decaying process.