Yes but actually no.
I don’t know if you use WarMode often but the best experiences are when the game turns into a tide reminiscent of the TarrenMill/Southshore battles and usually happens during the invasions.
The Darkshore Pre-patch showed even the availability of the net does not push for that dynamic to return as the most effective strategies rely on flying bands to swoop in and fly out of reach.
So yes, flying should be disabled for WarMode lest I wait for the next expansion to get a good experience out of it again.