Because Urouge knows nothing about the Straw Hats, his comments are based on assumptions (Zoro being a super nova with a bounty far higher than the others, for example). Of course he would conclude that Zoro is the second in command, while we all know that there is no real order within the crew. We frequently get to see the Straw hats from the pov of others, but merely to see how notorious they are (and of course for giggles, like Choppers or Sanji's wanted posters).Why in the world would Oda have one of his characters say something like Zoro' is the Second in command when he isn't.
I'm not considering Zoro (or any other SH) the first mate unless it is stated from someone within the crew (you know, the ones who can really judge).
And the only incident giving any "hint" is this one:
Luffy agree's that if he ever chickens out, Usopp is the new captain.
Fits your description:
After Captain, the most authority on a pirate ship had Quartermaster. As a Captain's right hand, he was in charge when Captain was not around. He had authority and he could punish men for not obeying commands.
Now you can argue that this was comic relief (although I see no laughs, no face faults, whatever). You can also speculate that after Usopp left, the "deal" is void as well. But we don't know that, all assumptions.
But whatever, Oda will never break the unique relationship between the Straw Hats by introducing Whitebeard-like rankings.
Edit: Btw, It really feels like people need a compensation for Zoro having "no real job" on the ship. The SH's give a damn about that, why should we? Zoro is Zoro and his worth is unquestionable. And something on topic: I don't think Blackbeard has a first mate as well. Because frankly, out of all pirate crews, his seems to be the closest to the Straw Hats (captain cares for his members, no real order spottable etc)