Considering she says the Warden is dear to her heart years after Origins, and considering we don't know if she and the Warden never once met at any point between DA:2 and Inquisition, I wouldn't say it's likely she believes the Warden to be dead. Wasn't her whole purpose of helping the Inquisition being to find the Warden, if she was romanced, to both gain the aid of the Warden against the demonic forces and to also be reunited with her lover?
I probably wouldn't mind her hitting on my Inquisitor, but my Warden Rogue would sob profusely, then kick Leliana in the shin, then sob some more. Having her as an option only if she was left unromanced, or was romanced and then hardened (since she gladly got into a threeway if hardened, she probably would've moved on from the Warden by now), that'd be fine.