Does hinderg terrian bonus count towards the rule of 3?

Energy shield +2
ICWO +1
Hindering Terrian +1
= +4 to defense. Yes or No?

no unfortunately the rule of 3 applies to defense as well so the most you can get out of that is a +3 to defense. you would be ebtter served using the ICWO bonus on something else in that situation

Does hindering terrain actually add to your Defense, or does it provide a penalty to the opponents Attack value?

It provides an increase to your defense value.

In the original example it would still be a good idea to add it to your defense...you never know when you might get charged and ESD & Hindering would mean squat.

This is one of the reasons why I would prefer rules that had some "modifiers" be applied to the attack roll rather than applying to combat values. Especially in the case of terrain and ranged combat attacks...it would trivialize the calculaction of Energy Explosion hits for instance.