The ports on the headers are for the A.I.R. system. Air pumps were installed in these trucks until 93 I believe. Most people remove them since newer catalytic converters are able to pull out more hydrocarbons and carbon monoxide gas than the old pellet style converter that would have been found originally on the truck. The A.I.R. system was no longer used when the new converters were used from the factory. I suspect that they will leave it as the vehicle has to retain all originally equipped emission control systems...minus the EGR of course.
Kind of stupid to retain old emissions equipment if technology has improved since then. The real test is the sniffer to pass emissions anyway.