Are annuities with named beneficiary considered part of the estate at death And is the executor entitled to a commission on that annuity?

No. When the decedent arranged for an account to pass to a named beneficiary on death the proceeds pass directly to the beneficiary upon the death of the decedent. Those proceeds are not a probate asset and this are not part of the probate estate.

For computation of tax purposes, the proceeds are counted in the gross estate. However, most estates in the US do not reach the threshold for paying an estate tax.