It's there. It's under the default player frame, or if you use unitframe addons, it usually shows up as part of the Totem Bar.
If you want a clear way of seeing when your runes are running out I'd suggest installing TellMeWhen, it's very easy to set up and looks great.
It doesn't show up for me either using Xperl. I just use NeedtoKnow. Wish it was a counter under our buff (like other buffs) in the standard buff UI.
WildStar -Mechari Medic, Draken Stalker
GW2 - Ranger