Ninja looting has for me, reduced the loot ratios for other people that follow in after. It doesnt reduce the spawn though. I think it's to stop organized groups rotating a single person through a max spawn dungeon every 15minutes and flooding the economy, if it is scripted this way (it makes sense), which we can only guess at, as detailing how it all works with confirmed facts could lead people to exploit it with reliability rather than guesswork.
If the exploiting of loot is only done by people following erratic patterns that happen to work from their perspective, its not going to be reliable but it satisfies those who think theyve nailed it down to a fine art because they could be hitting one of many mechanics that truly reset the area to a 'good loot' period.
My own opinion has always been, sure spawn affects the loot but, whether it's cleared by a ninja looter or a group, you have to be the first person to that dungeon after a reset and it has to be max spawn to have the potential to find anything good, and that personal unverified opinion hasn't done me wrong yet.
That aside, Perfidus, a difficult quandary to make suggestions around.
If each boss within held a key to one chest, it would encourage ninja looters that dont just stealth but have the skill to target each individual boss while ignoring the majority of the other enemies. The pickpocket checks are generally far lower than stealth checks, so attempting to steal the key successfully and escape if you are noticed can add a fun element to ninja looting.
If there was an area kill counter that triggered a chest to open, this might cause issues on lower spawns where there's not enough to kill, or people luring creatures through areas to add to the counter.
Chest value that scales to the encounter difficulty which the contents within are divided into from a table is already implemented I think so I dont need to suggest that.
There's also people that remember the good times of Perfidus, 'Good times' being before it was scaled down due to high appraise characters in groups turning the haul into 100k+ pure profit (this was said in a thread once, but I dont have a reference to that thread so take that with several grains of salt) that could be blaming ninja looters for a bad spawn, when really, it's just been scaled down compared to what it used to be.
Personally I'd like it if bosses had keys that held their own stash safe rather than them dropping it all, so you have to both kill the bosses and make it to the end, but this may dishearten people that stop halfway due to party limitations or casualties, and might cause people to hoard keys to hand to their ninja looters at a later date.
I keep talking down my own suggestions because, well, its already currently balanced so adjusting one thing affects several others, ack. Hrm..
If it's not already implemented, maybe once every 16-32 game hours, randomised since the chest was last opened that procured this effect, have the chest drop ONE item that is always higher than half the chest value, and divide the remainder, see what people think after they've been told the chests have been 'adjusted' to this or something similar, revert back to normal if people are unhappy, rebalance if people feel it's too good.