Thanks for reporting this issue. I still have loading times of only a few seconds in my playthroughs with 2k+ turrets, but I suppose with significantly more objects, such as on multiplayer maps, the list would get to be very large. It could also be that some modded object being tracked in your game has an unusually large table.
To fix this I could:
1.) Dump the list of tracked objects and re-search all entities on game load. It would mean the chests would stop functioning while the list is repopulated, and UPS/FPS might suffer for a while after game load. I'll try this out and see if it's a worthwhile tradeoff.
2.) Try and track only native types (i.e. coordinates of entities instead of the entity tables) in the queues and use the native types to populate entity lists. I hesitate to do this because it could mean a significant hit to performance for the mod, and I just got the performance down to an acceptable level as it is. If option 1 doesn't work out I'll consider it though.
I'll work on it this upcoming weekend and let you know what I find.