Spy kits now have a 60s recharge, meaning it's completely impossible to maintain them (much like everything else in this game...) - what implications does this have for dungeon runs?
Ash Legion Spy Kits are still excellent for breaking aggro when you're being chased, but they're no longer very useful for reviving a defeated player in the middle of a group of enemies. You can still use them to get communing skill points and such though, so by no means should you throw them away. Note that they now require you to activate a skill (which you get after using the consumable) with a 0.5s cast time.
Order of Whispers Spy Kits, on the other hand... as far as I can tell, they're useless. You could chain them with the Ash Legion kits, but 13s of stealth is not going to make much of a difference, since you still have 47s downtime. Unless someone can think of a good reason to hang on to them, you might as well trash these.
I think the main change this effects is that thieves will now be more useful in dungeons. Shadow Refuge has always been good for stealthing downed people, but now it's the only real way to stealth yourself (and others) for a considerable duration. That said, it's not perma stealth (unless multiple thieves chain it), so reviving people once they're completely defeated is going to be a lot more of a nuisance. So don't suck while running through stuff, don't get yourself killed, and if someone on your team goes down, go revive them quickly.