War ops have the odds stacked massively against them.
Stealth ops might be a 6v6 stealth operation. War ops might be a 6v60 full combat operation where the 60 have 20 minutes' advance warning to prepare. That is gonna be some steep odds no matter what gear you have.
Experienced players know that war ops generally does not win, and thus, they will push for stealth ops. The result is that war op teams tend to be dominated by newer op players, and/or op players who don't actually care about winning. This further reinforces the fact they are unlikely to win.
Ultimately, the ops' ammo and weapons are finite, whereas the crew can clone, use pets, golems, etc. Further, the crew controls the location of the disk, which means the ops have to come to them, through their defenses. The longer a nuke op round lasts, the better armed and more prepared the crew, while the more of the ops' resources are depleted. So, a quick stealthy smash-and-grab is always going to be more effective than a full-on drawn out military siege. Once the nukies' comms are compromised, they can't even co-ordinate effectively.
The tactics that work during stealth, or surprise ops, like having one person create a distraction, simply don't work during war ops. A lone op somewhere else can create a distraction for a few minutes, but eventually, crew will kill them. In stealth/surprise ops this does not matter since you'll hopefully have the disk by then. In war ops it means you're down a player without reducing the strength of the crew significantly.
For all these reasons and more, war ops are at a BIG disadvantage, to the point that many admins (including me) outright refuse to send ERTs during nuke ops, because we reason that the ops have little chance of winning even without an ERT / etc helping the crew.
I'm not sure what could be done to make war ops a fairer fight... or even if we should make it one (truly a 6v60 fight where the 6 win may not be satisfying to most players). It definitely isn't a fair fight as things stand, though.
Of all the ideas I've heard to make war ops a fairer fight, perhaps the one I like best is: upon declaration of war, turn 1-3 crew into traitors with objectives to assassinate different members of Command. This way, we're discouraging the HoP/Cap from giving everyone guns and all-access, without outright prohibiting it. We're also evening the balance in the number of players on each side, a little, and ensuring that the crew doesn't have 20 minutes' hassle-free prep time. Rather than outright prohibiting anything or making it impossible, we're introducing some disincentives that curb the most problematic behavior on the crew side, and even up the fight, without making anything totally impossible.