Is there a console command to remove all dead bodies/creatures in the world?

Not that I am aware of, but if you rest/wait 3 days in a different cell, all non-permanent corpses should disappear.

I don't think so, because some dead bodies is a quest object and shouldn't be altered via the console.

Ok I'll give that a try thanks. Out of curiosity, how big is a cell? How many cells would Balmora cover?

Some pre-placed dead bodies are "perma-corpses", and will never disappear, such as a particular tax collector or others with names such as "corpse" or "dead adventurer". Amusingly enough, they can be used for safe long-term storage of your belongings.

Bodies of NPCs and creatures that are killed in the game will vanish on their own after 3 days, along with any items on them, if you're away from the area. You can also select most corpses and choose to remove them, which happens immediately; any items on the body will automatically be placed in your inventory. Creatures or un-named NPCs (guards, etc.) will respawn the next time the cell is reloaded, including if you save and reload while in the same cell (which makes it a good idea to delete corpses on your way OUT of a dungeon, not on the way in, unless you like fighting everything twice). Outdoors, I believe that you have to be at least 2-3 cells away from the site for the cell to reload, otherwise it's still close enough to stay "loaded". Going from Balmora to another town (Pelagiad, Caldera) would be far enough, but hanging around just outside the town walls won't work.

Not positive without looking at the Construction Set, but I'm assuming that Balmora is mostly in one cell, or else straddles the line between two cells. A cell is pretty big, and the game has to load the cell you're in, plus all of the adjacent cells, and MIGHT load portions of the ones surrounding that as well. Note that when you cross the border into an adjacent cell, there's sometimes a short pause while the game loads the NEXT cell beyond the one you're entering. Obviously it has to load the adjacent cells, otherwise you could be next to the boundary and everything 2 feet away in one direction would either be blocky and undetailed or else missing completely. Stepping those 2 feet closer would suddenly make things appear or jump into higher resolution. Picture a 3x3 group of squares, with you in the center square; you can be anywhere in that center square and still have a full cell between you and empty space; crossing the line into the next cell updates which ones are loaded by the game, so you're again in the center.

Thanks, if I'm in Balmora and enter the fighters guild, does that count as a different cell from Balmora?

Yes it does.

All interiors are one individual cell.
Exterior cells are different. The exterior of Balmora is about two cells, but the 8 surrounding cells are also loaded. If you use MGE for Distant Land, then more will be loaded obviously.

So yeah, like mentioned, go into a building and wait 72 hours to clean away dead bodies. It's a good habit to get into if you've been playing for a long time.