Actually, it doesn't hit each time you go through the warp point. There is some random factor that determines whether your ship gets damaged by the warp point or not. Sometimes you can pass right through without anything happening.
[ 09 January 2002: Message edited by: Imperator Fyron ]
Also, IIRC with damaging warp points "size DOES matter". ISTR that escorts and destroyers will go thru certain(but not all) WP's without taking damage - even without armor.