(Answer updated for Phantom Liberty)
There are enemies immune to quickhacks, but they are generally plot-critical (or the quickhack would not make sense against them). For example, in the final race of The Beast In Me, you cannot quickhack Sampson's car for reasons that will quickly become clear if you've never done that quest before. Another example is you can't use the Bait quickhack on an enemy who's standing on the opposite side of a waterway. Aside from these, the most important enemy that is "immune" to quickhacks are minibosses, against which the instant-death quickhacks System Reset & Suicide might not work, (although you are annoyingly still able to use these quickhacks, they just have no effect).
That said, the game did change substantially in that it's no longer possible to kill most enemies with a 1-RAM cost quickhack. A simple Short Circuit will now generally cost 8-10 RAM. In compensation you have more RAM total & RAM regeneration is faster, so you can still queue 3+ Short Circuits on one target to ensure they die, but there's not enough RAM if you're fighting several enemies at the same time. This means that an alternative weapon is more important than before.
As with pre-Phantom Liberty, which alternative weapon you use is up to you. The Intelligence tree remains necessary for a quickhack build, and it incidentally buffs Smart weapons, so that's the natural choice, but there are plenty of alternatives. Besides, you have enough attribute points to max three (and nearly a fourth) if you wish. You're not constrained to smart weapons; you can use whatever blows your hair.
That leaves the question of whether one of your three maxed attributes should be Reflexes. Suffice to say it doesn't really matter. Reflexes does add to your quickhack damage (since there's a cyberware upgrade that lets your quickhacks critical hit), and I've found the ability to dash to be a major convenience, but ultimately it's up to your playstyle. If you like quickhacks, definitely max Intelligence, and the rest is up to you.