We already know that there are some major changes coming to raiding in Warlords of Draenor -- specifically the shifting of what LFR, Flex, Normal, and Heroic raiding means to us right now. With raiding changes often come loot changes, and folks are understandably nervous about how loot could work in the future, considering that all new raiding modes save Mythic will have a cross-realm option.
Never fear, it's Ghostcrawler to the rescue, with loot question clarifications. It seems likely that bonus loot rolls aren't going anywhere. Right now you can roll for bonus loot on any boss, including Heroic, and it looks as if at least that will continue. We don't know about it continuing into Mythic level raiding, however we have no indication either way.