Yes, friendly fire is very annoying in Mario Kart 8 Wii U, especially since the bots still target you with Red Shells even if they're on the same team as you.
However, they made some adjustments to the way some items work in Deluxe's team races. Red Shells only home in on racers from the other team, Blue Shells once again target the leader of the opposing team, Bob-ombs won't explode when a teammate approaches them, Piranha Plants won't try to bite your teammates, and Boo only steals an item from an opposing team's racer.
I liked Mario Kart Wii's team mode with the exception of the Lightning item being even more overpowered (both versions of 8 also have this problem). In my opinion, MK7 had the perfect team mode. Red and Blue shells act like how they do in 8 Deluxe, and Lightning affects everybody.