title explains it all pretty much, let admins access others enderchests even though they are not online.

I don't believe there's an easy way to make this happen currently, the ability to access a player's enderchest is made possible by the owner being online.

This would require to save ender chests in files.

Wouldn't it be possible to save the enderchests in the playerdata files for Essentials though?

Sure, this is possible. However, this is a huge amount of data there. ItemStacks, ItemMetas, nbts...

Shouldn't it be saved in your main world's "playerdata" folder already? But I don't know how accessible those files are. Anyway, if you're considering /ec for offline players, I'd love to see /invsee for offline players as well.

Minecraft's player data is saved as .dat file, which are a bit hard to read.

This probably won't be implemented any time soon, as there isn't a way to get the inventory of offline players through bukkit.