I'm tossing into this argument as a Pro-Morri/Leli romance!
Except not with the Inquisitor, as let's say either Morri/Leli were romanced and for some reason in the game the warden 'makes an appearance' either from far away or whatever. Then I damn well want to see them kissing said Warden! And yeah... that's about it.
Though, as for the Warden vanishing, I'm damn near certain that has something to do with Flemeth one way or another. At the end of Witch Hunt you can travel with Morrigan hells knows where (Beyond the fade, whatever that means). Given the events in Masked Empire this likely just means really effing far away. I'm curious why Morrigan ditched the potential OGB, and if the Warden followed her, him as well.
Now, if they weren't romanced/ect, then you can easily do the one night stand thing, or my favorite, 'married to the job' and just tell us to bugger off. Perfectly acceptable.
At the end of the day, it's just easier and consumes less of their limited resources to just not do anything with them. Also, pitchforks.