I personally have not found any boss ships in Valencia and I don't think there are any. This may be for many reasons. I think it is because it is harder to justify random very powerful ships in the armada since they are so uniform they would send there powerful ships to the most important parts of their conquest and the majority of there ships are the same since they are all manufactured the same. This is probably why the armada does not produce a boss ship in any other part of the game as well i.e. Marleybone. This may change and even in Valencia as we clash more with the armada head on, and some people believe we will be heading back to Valencia in the next update and since there is an unopened skyway there it is possible a boss ship or two is there.
dont forget the trip to valencia is undercover. you were supposed to sneak in, do your job quickly and then leave as fast as you can. dont forget its only a little bit of valencia. there could be boss ships when we go in deeper. think of it as a video game demo. you get to play it, but you can only play a little bit