358/2 Days Another theory...

Even though the replica may or may not really be a nobody (though it has been pointed out that replicas do have hearts), the Organization wouldn't let just any Nobody join them.

 

Aqua can use the Keyblade....

 

What does that have to do with letting her join? Plus, doesn't Roxas already use keyblades?

 

The more Keyblades the better.

 

That may be your choice, however that may not be the same as the Organization's

 

Because the organization's quest was to get as many hearts from heartless as possible. Although the other org members' weapons were able to kill heartless, the keyblade was created specifically to

1. Lock worlds
2. defeat heartless (or unlocking locks)

 

However, you said yourself that the other weapons are able to kill heartless. This does bring up the possibility of another keyblade, but I am still against this.