Templates can not hit flyers, unfortunately. However, I can tell you that the "Flying Circus" Necron list is not unbeatable. I just came from a local tournament where everybody was expecting the Necron flyers to just walk away with first place, but that didn't happen. I'm still wrapping my mind around this fact since I don't usually do very well at tournaments, but I actually won! I wasn't playing Tau, I was playing my Chaos Daemons, but I faced the Flying Circus in the first round, and he only won by the tertiary objective of killing more characters than I did. Details of my list don't belong here (I'll probably post a battle report or analysis when I'm less tired), but it was heavy to Tzeentch units packing Breath of Chaos and had lots of small horror squads. Anyway, the weakness of a flyer-heavy list is that there is a rule somewhere that if you ever have all of your units off the field after the first turn, that's considered a Tabling, even if you still have things in reserve. Knowing what was coming at him (lots and lots of Daemonic shooting), my opponent deployed far more on the table at the start of the game than he would have normally: three of five troop squads and his HQ, I think, and I still almost tabled him. Counting some poor Everliving /
We'll Be Back Reanimation Protocol rolls, I had him down to 4 models before the flyers showed up.
THAT is the weakness of a flyer-centric list. If there are just a few flyers, then particularly the Tau with there large amount of strength 6 or 7 crisis suit weapons and twinlinked railguns will have an easier time than most taking them down. If the list is very heavy to flyers, then, again, Tau have a better-than-average chance of eliminating the ground forces before the reserves arrive.