Good evening ! I've been scrutinizing the ships advanced attributes and I realized two hyperion energy shield modules have a defense of 86% while the defense of three modules is 90%. On the other hand, if I put a plate defense instead of the third energy module, I get 49% armor defense and keep the 86% energy defense. So, my guess is that, overall, a mix of defenses (and probably weapons) is better right ? 

Shields don't provide as much bang for their buck as Hull Plating, as Hull Plating can almost entirely negate both energy and kinetic weapons later game.

I tend to use mostly hull, and most times one or two shields. I'm not playing competitive though. Vs. AI on endless difficulty it's enough like this.

Bottom line is, it is better to use mixed defenses, unless you know what you have to counter.

Yeah the advantage of plating is that there's usually more of it and everything has to go through it anyway so it's reliable...but it takes time or dust to repair.  Shields on the other hand are easily countered but regenerate automatically without needing all those turns.  I usually try to have at least one shield module on every ship so that if they run into any light resistance along the way, the minor damage they take doesn't add up to leave them damaged for the real battle.