I've been reading this and finally got a chance to write on something not a mobile device, so I do have a few thoughts.
First off, about what Obi said about honor and battle, fact is, there's way to gain honor that doesn't involve combat. And also, combat itself and even victory isn't an honor guarantee. Goerge W Bush went to war with Iraq and won it, but he wound up getting tarred and feathered over it.
And while I do agree with Ridik's approach, I believe it up to a certain point, and some of the current espionage endeavors actually cross that line. I don't think spy work and sabotage itself isn't bad, I don't mind it when there's a way to do it within the game itself, and it's success is more dependent on skill rather than exploiting. Allow me to explain.
When I played Planetside, I usually was in an infiltrator suit, which allows it's user to go invisible, but I would have a faint outline which would appear depending on how much I moved. I used this suit often to get into bases and hack them to disrupt the enemy, stole vehicles(once stole thier version of a mech, man was that fun!), and caused general havok. But ontop of the glowing problem, the enemy had which was a close ranged implant that allowed a person to see me when I was cloaked, and I had a limited stash and weak armor. Starcraft II has Overseers which can gunk up buildings and send in changlings to look like troops, but were unarmed and usually used to detect cloaked stuff. C&C Red Alert 2 has spies which could sneak into a base and cause havoc, but you had to watch out because Fido had no problem using him as a doggie biscuit. All had balance in the game and enhanced it.
The problem with Starmade is though, there isn't any real way to deal with spies rather than making things harder on factions by having to implement screening measures. I don't like the direction of this and I have my concerns about how much this faction update can solve them. Even if you can restrict block access to certain groups, you wind up needing to create a more restricted environment to do so, blocking access to resources to key people and playing a trust game. Plus, you have that whole mutiny fiasco which went down a few months ago, and if it is true, the RA getting tampered with attempts to destroy the faction from the inside.
My worries is this game might be going the way of Magic: The Gathering and Yu-Gi-Oh's One-Turn-Kill Decks. Basically, MTG's legacy mode and quite a few Yu-Gi-Oh decks are focused on the concept of killing your opponent before he gets a turn, pretty much turning the game into a glorified coin-flip wins. Granted, they aren't surefire methods, but it really goes against the concept of trying to compete against your opponent. Rather in Star-Made's case, this spy problem risks turning the game into a glorified Mafia game. Mafia is a forum based game where you try to find the Mafia members hidden with the townsfolk. Each day you kill off a person and the goal is either to kill of the scum or survive till the end. It turns into alot of politics, and ugh...
I understand that you're going to have politics when you have factions, clans or whatnot, but I really don't want to see Starmade get turned into Scummade with sabotage that can't be controlled or balancing it with making things harder on us. I can't see requiring people to chat over voice being the balance, since if there's someone you never heard the voice of before, how would you know the guy's scum or not? Where's the fun in being worried about assigning your members ships and whatnot and having to make sure they are going to come back with it? What's exciting about trying to pick out that one guy and maybe hope he won't go to give your recipes to someone? I know things like this happen in IRL, but do we not play games to get away from this? Even in the real world, there's tactics that are never used before they are though of as unacceptable, we call em WMDs.
Perhaps should we consider ways to curtail it, or maybe look into ways to allow someone to sneak around like in Planetside and perform some intel runs or maybe toy around with the enemy's base, but have have to catch em and it's up to the players if they can get the object or catch the inflitrator?