Just went over there. I had to listen to everyone moan about the war, and then wait 8 hours, and then listen to an argument between Madena and the Jarl, then she finally went behind the counter (9 am-ish) and offered to sell stuff.
Sadly, when my favourite shopkeeper, the twinkly-eyed bearded blacksmith at Whiterun, went missing, it turned out to be Vampires, and by the time it dawned on me that I could have saved him, it was far too late. If anyone knows a console command to get him back, that would be good, as he always had plenty of money too.