The holes you are referring to ARE access holes to the EGR exhaust ports as previously stated. The ports inside the manifold are different size orifices to distrubute the emmissons equally. After years of use the holes tend to become clogged and have a tendency to limit the exit of emissions, causing failure of smog checks. If sometime in the future that you find you can not pass smog checks, it is a good idea to take the manifold to a shop to remove the plugs, ( the man' has to be heated with a torch to remove the plugs, otherwise the steel plugs will strip the alum, manifold) and have orifices cleaned to better distribute the emissions from the EGR.
Been there Done that====results smog check passed A++++