Arcane hydra does AoE damage, while basic, fire hydra, only does direct attacks. Tooltips have same basic damage. Do arcane hydras have drawbacks on single target (like slower fire) or they are plain better than fire in all aspects (not taking in account passive skill effects or some arcane/fire skills synergy)?
In general, there's no reason to use unruned skills as runes will always provide an advantage over the basic skill. In this specific case; yes apart from potential effects of Conflagration there is no drawback to using Arcane Hydra instead of Fire Hydra.
Prior to 1.0.3, it would have done less damage vs Molten or Fire Chains elites, which is no longer applicable. Also, inferno zombies used to be resistant to fire as well - no idea if that is still the case, but afaik Blizzard has removed all monster resistances post-1.0.3