Has Energy Explosion EVER had the rule that the damage was penetrating or unavoidable; that it could not be reduced by Toughness, Impervious or Invulnerability?

No.

At times, you were able to combine it with things like Enhancement or SHIELD TA for a damage boost... but it was always plain, ol' damage dealt.

I don't think so. I went through the older rulebooks (thanks to Supergene's archives), and I didn't find any mention of this.
Moreover, in the first rulebook, it is made mention of damage-reducing powers in the text of EE itself:

"ENERGY EXPLOSION. This character's ranged combat attack can affect all
characters in base contact with the target. (Optional) Give this character a
ranged combat action and reduce its damage value to 1. Make only one attack
dice roll. Compare that result to the defense of the target character and every
character in base contact with the target character. A successful ranged combat
attack inflicts 1 click of damage on each character hit, causing knockback, if
applicable. If this character misses its primary target, it misses adjacent figures
as well. “Splash damage” is only triggered by a successful attack on the declared
target. If a figure with this power can attack multiple targets, Energy Explosion
can be used to target all of them. All the damage done by each “explosion” takes
place at the same time, so damage-reducing powers (like Toughness and
Invulnerability) may only stop part of the total damage."

All right, that's what I thought. Thank you both for helping me win my argument.