Only if they aren't suefluenced, probably. A big difference between medium awareness and omniscience is that a medium-aware character is still at the whims of the plot; they may not know what else is going on in their OWN story or be able to manipulate their medium ('skip ahead chapters') in a way that could reveal things. The fact that a character might be a Mary Sue or an agent might be there may not occur to them because for all purposes they have the same perception as a normal person even if they have 'insider' medium-knowledge.

In short, while they may know they're in a story, they are still in the story and wouldn't know what's going on in scenes where they aren't there, or know that the PPC is part of the medium they're familiar with in the first place.

Besides, lots of characters like this are aware for purposes of humor. So while they might be able to wink sideways at the audience, they'd only be able to do it if it's funny.

So Pinkie Pie might be able to make a gag at the agents, but only after she's no longer OOC and only when it's funny. Being able to simply see through a SEP field may, or may not be funny. Besides, we aren't part of HER medium; we're practically invaders. So while she might be aware that she lives in a cartoon, she might not know WHAT cartoon or that the PPC exists at all.