This is another sitaution where I've seen the good and the bad sides of some of these sitautions. I've Mu*ed on various games with my partner for a good many years. Yes, we have some characters who have come together as couples, but usually we have far more non-partnered characters. Do our alts come across each other? Sure. It happens.
I don't really see an issue with it, so long as you have a wider RP pool than just your partner. (The same goes for Rping with your friends, tbh.) In fact, most of my characters, even those in relationships, Rp more with people outside of their relationships than they do within them. But I might just be an oddball in that regard.
Alas, I've also experienced some bad OOC reactions from other players when it comes to playing on the same game as my partner. The worst being when the sins of one partner being taken out on another. (Your partner said this and you didn't tell him to stop so you must be horrible too! or I hate so-and-so and you're married to them so I won't RP with you/interact with you/let you progress either!)
In any case, no, I don't think that couples should be treated as alts for each other. As others have said, it's no different than friends playing together. But honestly, I'm an individual, and I prefer to be judged by my individual RP and actions, not by my connection to my partner.