Do damage rig effects stack with non-rig damage modules without penalty

The stacking penalty applies to the bonus, not to the module.

If you have a thermal hardener and an EM hardener fitted, both would provide the full resist bonus. If you add omni-resist plating, its thermal and EM bonuses would be reduced because of the stacking penalty, but its explosive and kinetic bonuses would not.

The precise formula is somewhat complicated, but it can be summarized as:

1. The first module provides 100% of its bonus.
2. The second provides ~87% of its bonus.
3. The third provides ~57% of its bonus.
4. The fourth provides ~28% of its bonus.
5. The fifth ensures your fit gets posted in a "fail fits" thread on the forums.

The order you fit the modules doesn't matter; the one with the largest bonus will always be considered "first".

Some modules (notably Damage Control Units) are exempt from stacking penalties.

You are incorrect on one point. If sig radius is equal to or grater than your explosion radius you do 100% of the damage. If it is smaller it is reduced.

This means that any sig radius above the explosion radius is doing you no good.

The actual formula is:

Damage = Base_Damage * MIN(MIN(sig/Er,1) , (Ev/Er * sig/vel)^(log(drf) / log(5.5)) )

Where sig = ship's signature vel = ship's velocity Er = Explosion Radius of missile Ev = Explosion Velocity of missile drf = Damage Reduction Factor of missile

The log function is the natural logarithm, to the base e, often denoted as ln.

The 5.5 in the equation is the hidden missile attribute "oaeDamageReductionSensitivity" which you can see in the QR SQL data dump (can also see it in tools like EVEmon).

Reference