The Thieves Guild may not neccesarily be one entity, but a collection of smaller guilds and groups that are loosely connected.
The Riften based Thieves Guild may not be even remotely connected to the Cyrodil branch, beyond basic 'ambassador' operatives that carry information between groups about artifacts, blacklisted members and even organisations that may be cracking down on the thieves.
Who's to say the Cowl still remains in the hands of the Cyrodil guild. It may have been lost, destroyed, Nocturnal may have even found a way to get it back.