Are the antenna diodes only there to reduce damage during manufacture or is there also impact runtime in an electromagnetic noisy environment?

The antenna diodes are only relevant during manufacturing, when a metal line is connected on one end but not the other. ESD diodes on the other hand protect inputs against electrostatic discharge when the chip is in use.

There is a tiny amount of extra capacitance on the net because of the reverse-biased junction of the antenna diode, but that's it. These diodes do get taken into account in when determining timing though.

I thought they were there to allow Van Eck phreaking of the processor state