Let me give you a few examples.
1) If you take everything on the table in the room with hrisskar's note (the chargen stuff) and pile it up in the corner of the room, then you delete that cell using EE, the pile of stuff will be gone and everything will be back where it was the next time you visit that cell. To my knowledge this just applies to what is laying out, nothing in containers should be affected, because there is a separate entry for containers altered by player.
2) The same applies to mod-added cells. If you've added/moved/taken items out of a mod-added cell, it will be returned to it's default state also. Everything you left laying out will be deleted and it will reappear back in it's original location.
3) The same applies to exterior cells. If it was on the ground and you picked it up and dropped it three feet away or kept it, it will be back in it's original spot after that cell has been deleted.
4) This won't affect NPC's or their inventories; Fargoth's ring will not re-appear in the barrel and NPC's you've killed will not be resurrected.
As you might expect, this can result in some unbalancing and extra loot ingame, but that doesn't usually bother me.
What I mean is, if you run Lilarcor and have it/him in your inventory when you delete cells, he'll be back in Arrille's tradehouse jabbering away the next time you go in. Thus, you can potentially own two loundmouthed, annoying, uber-swords, insead of just one. This is not doubling, exactly, because there are not two of the same thing in the same place anymore. There's just one in your inventory, or in a container, and one in it's original spot. Did I just muddy the waters more?
The thing is, the items are technically deleted, but they show back up at their original locations. Nothing in your inventory should be affected, nor NPCs or anything in containers, because those have completely separate entries in EE. In EE, under 'cells altered by player' you can pick and choose which cells to delete. If you know of cells you have redecorated and don't want changed, you can UNCHECK them and they won't be deleted.
You might want to back up your savegame and play around with EE a bit. As I said, my first experience with EE was deleting everything under the 'stolen items' heading. I was tired of taking a piece of paper and from then on having every piece of paper in the game marked as stolen from 'a shady smuggler'
As far as the doubling goes, external and internal, if deleting the cells doesn't work, I'm out of ideas.
Just out of curiosity, have you tried unchecking GS_Seyda Neen Complete.esp, saving your game without it (a clean save), doing a repair all in wrye, and then re-checking the mod and continuing on? This will reset EVERYTHING that is added by that mod, but only what is added by that mod. If that's acceptable, it should solve your doubling and FPS problem in Seyda Neen.