I thought so too. It's not entirely clear why Nick had such a vendetta against that Ennis guy, so I assumed that might have been because he killed Madison, or at least had an involvement in her "death". It seemed like more of a personal conflict rather than a vendetta against the Vultures as a whole. Like you said, Madison has only appeared in flashbacks so far. She's due to make appearances in the next few episodes, but I'm not sure if those take place in flashback-land or if they take place after Nick's death.
I figured there was some kind of symbolism behind those blue flowers (forgot their name) and I assumed that they were supposed to represent Madison since they're present once when Madison is there and once when she's not; the latter being when Nick seems to pay particular attention to them. Madison's the main character so I'd assume she's got plot-armor, but that hasn't stopped TWD in the past (looking at you Telltale). I'd say it's unlikely she's dead since I personally think the show would kinda fall apart without her since she's pretty much what ties everybody together. But I dunno.