I noticed quite a few times when I was making up ion defence effects for some turrets that the actual % defence given wasn't matching what the % listed in the structure tab was showing. After doing some testing and number crunching I figured it out.
I had a ship with 7642 blocks but only 218.7 mass. There was 25 ion effect modules with a mass of 2.5.
The structure tab was showing around 3.9% effect and when I activated it I got 13.7% effect show on screen and damage indicated when shot was reduced by 13.7%.
The structure tab is calculating the % effect from the block count or is assuming all blocks are the same mass.
Where 5% of blocks gives 60% ion defence.
ion blocks / total blocks / 5 x 60 = 0.039 = 3.9%
Actual % is based on mass
Where 2.5 mass ion blocks out of 218.7 mass total
ion mass / total mass / 5 * 60 = 0.137 = 13.7%
I didn't check the structure tab for any of the other defence effects % if they had the same issue.