Replicators can indeed create materials beyond what some people seem to consider 'basic' (we've seen it happen numerous times and was confirmed by dialogue even in TNG).
As for the mobile emitter ... well, it's possible the thing was non-replicable due to the poly-dutonic alloy and various other materials it had (elements that Voyagers computer couldn't make heads or tails of because they haven't been discovered yet).
The device in DS9 was probably not that complex to understand by the station's computers.
Just because our heroes never thought of a way to create such a device (and why would they in the first place?) doesn't mean they couldn't if the didn't set their minds to it.
Furthermore, the technology and materials behind the device in question were not of futuristic origin like the mobile-emitter which was after all 29th century technology.
Keep in mind that Starling most likely created the mobile emitter using the Timeship's own mini-replicator (which it probably had and was already centuries ahead of what Voyager's replicators could do).
Furthermore ... Starling may have used 29th century technology as a way to jump start tech development in the late 20th century, however, several possibilities could have occurred:
1. He couldn't understand most of the tech and therefore couldn't create anything new.
2. He already developed and had in mind to put forth products that would bring him in money for the next 20 years, but decided to make more profit by putting them out in smaller numbers.
His statement on the other hand that he used the timeship as much as he could for innovation speaks for itself.
He didn't understand most of it and barely scratched the surface with his developments (going into the future to get more technology would only get him so far because most of it is already integrated inside the ship).
