It happens. There's a command out there to restore an NPC back to life. But I'm not sure how far along you are on the quests as Aela does have some part in them. You can also choose to find another steward from some of the other NPC's that will follow you. When you take them to your home, check the dialog with them. Sometimes you'll get the option for them to watch your house for you.
As far as where she might be, go all through Jorrvaskr to see if she's there. Check at the dinner table and sometimes in the chairs off to the left when you come into the place. Check out back, up at the skyforge and at the underforge if you've gotten that far.
If she's missing (and no corpse is visible), then she's probably lost in transit to the dungeon you were going to. If reloading before you traveled is impossible, then check the route between Whiterun and the dungeon. Sometimes, NPCs won't fast travel, and might, instead, walk there. It's a frustrating bug that I seen happen before.
+O2baguru I looked ALL OVER whiterun, the house, jorrvaskr, even the underforge... and im finished the companions quest and i went to this place to collect the totem of hirccin and i wanted to kill the bandit cheif with no weapons, (i am a khajiit) so i could get an unarmed kill-cam, and it took like 5 min, and i got the totem, but no aela. and i didnt notice this until i was at jorrvaskr. so i went and looked in the underforge, at the house, and i cant find her. AND i cant use the revive command because im on PS3