Probably the only thing wrong with the ninja loot system 'may' (and I firmly emphasise and underline 'may' in this case) be an ignorance on how ninja looting works on this server, and why it is viewed as a valid playstyle. Simply put, the server is designed to allow it, and has systems in place to make it work.
If a person ninjaloots a dungeon, that loot will reset in fifteen minutes to match the strength of the spawn. It will not affect the spawn, it won't harm it, it won't weaken it. But if someone -returns- to the dungeon - be they a ninja looter OR someone who fought through the dungeon a couple of days ago - then the spawn is nuked back to its lowest rating and the loot is also reset. To prevent this, the server must be reset.
Simply put - dungeons can be run, OR ninjalooted, by a person ONCE PER RESET. To return to do either before the reset takes place reduces the spawn to base to prevent dungeon camping. AFAIK.
So, we have a twofold problem. One, server resets are now far less frequent than they have ever been. Two, people are not aware that a server reset is what is needed to prevent a spawn reset by going to the dungeon twice in a single reset. That's much more likely the cause of your grief than ninja looters hitting dungeons just ahead of you.