A bit of a counterpoint, as one of knikpiw's players:
I feel System Override is overpowered when you use it to shut down the nearest shield facing immediately before shooting at that side of the enemy ship (other uses of the exploit are fine, or maybe even weak). If the target's main (or only!) SOAK is from their shields, you've just negated it for free, and can keep on doing it again each turn indefinitely (as long as the attacker can beat E-DEFENSE). I think it's much stronger in this role for NPC ships played by the GM, since they take all their actions at once. It's not quite as good for player characters, as their teammates actions will spread out by their initiatives. If the character with the exploit ends up just before the target ship in initiative order, it's mostly useless (since they'll rotate to present a different shield facing before anyone can shoot).
But while System Override is often strong, Counterhack seems pretty weak. Mostly it's an issue of how narrow it is, and the opportunity cost of picking it over some other exploit that might apply more often. It only makes sense to pick it as a universal exploit if you know, in advance, that you'll be facing enemies with System Override. But how would you know that? If the enemy knew you were going to have Counterhack, they'd probably pick a different exploit for themselves! I was tempted to take Counterhack when I first created my character (who is very good at computers), but decided not too because I didn't think system override would come up often. Sure enough, it only came up this past session for the first time in our year-long campaign.
I suggest that both exploits be generalized. That is, rather than having special unique effects, they should tie in more closely with the normal rules for space combat. Make System Override give a +2d6 to ewar attacks or damage (with maybe the current exploit's effects on a critical hit). Counterhack in turn should let you use a reaction to roll your own ewar attack against anyone who makes one against your ship. The original attack and your counter attack would be opposed rolls, rather than being compared against E-DEFENSE.
In general, I hope the space combat rules will get an update at some point, as there are a whole lot of pieces of the system that don't really feel like they work well for small ships. Maybe with Class XII cruisers there's better balance, but space combat in our campaign with a couple of different Class III ships always felt awkward (e.g. either one or both sides struggled to achieve anything in almost ever fight).