Assuming we're talking single player:

When players first save the game, it makes a copy of the entire module in the save file. Subsequent saves update that copy - the module is never referenced again.

So, anyone playing version 1 will see no change when version 2 is published, until they start a new game.

The classic way to expand the world is to publish a series of modules. At the end of module 1, the state of play is saved, typically in a data base, so that when module 2 is published, the player can resume. Often, module 2 will include copies of areas from module 1, but they are entirely new instances - for example, chests looted in module 1 will be unopened in module 2, even if they're exact copies. You're free to change the tiles, objects and loot in module 2.

P.S. The above is only true of .mod files. If you have custom content, such as .hak files, they are reloaded every time a saved game is loaded. If you update a hak, players see the change on the next load. This isn't a problem - usually version 2 of a hak will simply add new content that is only referenced by module version 2, or benign bug fixes. Just be careful not to ever delete custom content, in case saved games require it.

The game save contains the entire module and any updates you upload will never make it to their saved game, they'll have to start a new game.
Updates to haks will take effect on their saved games and since stuff in haks override stuff in the module you can update anything that goes fits into a hak and see the update even in saved games.

Like in the Original a player can play through a series of modules and you could create this hook in a module you release before the next module is completely finished - and finish and upload this sequel at a later date. You could make a series of modules in this way

It should be possible to make some changes to an existing module using databases. The database files exist outside of the module so changes to the database can affect saves. I've used it in the past to make persistent storage for a "home" module. I've only really used it for objects and variables. The EE added some new area manipulation functions, so I don't know if you can use databases for areas too, but it's something you can play around with. It might even be efficient if you're trying something like a NWN2:Storm of Zehir overland map.

That said, creating a series of modules will probably be an easier and more robust approach for anything else.