So the rudder pin hole in the fiberglass lip provides no additional lateral stability for the rudder castings?
The hole was typically cut out in just the rear, so that side-to-side, the hole would still provide some support.
In other words, the gudgeons are doing all the work?
Pretty much.
Should I shorten the rudder pins then?
Why would you do that? The upper gudgeon is right below the deck lip. How would you get a cotter pin through the rudder pin with the deck lip in the way? You'd only be able to cut about an inch off the pin anyway. Trying to save weight?
The bottom line - if you want to fix the deck lip, fix it - recognizing that it's mostly cosmetic. Otherwise, leave well enough alone.
Pics would be really helpful here.