Our gm has even gone so far now as to require us to do a 'luck roll' to see if anything goes wrong, since with a well-thought out plan and a good hacker, things are 'too easy'.
Hacking with finesse takes a long time and hackers cannot find everything. It takes an hour per extended roll to properly hack into a node without brute force. IC and spiders make a hacker's life difficult as possible throwing black hammers around. Meat bodies are always at a threat of being taken/injured/killed while the hacker is in cold or hot sim. Being in hot sim for extended periods of time without food or water could cause dehydration, starvation, or addiction—and not to mention the terrible addiction side effects of a hacker in hot sim for too long.
There are always measures that can be brought against the hacker if he is having an easy time. It is true that no team is complete without a competent hacker or rigger: just as the crew needs a face, combat monster, or some sort of astral combatant. It is all about party dynamics. Other characters can do surveillance, walk a beat and pick up rumours, spy astrally, or bribe security or wageslaves to get access information, floor plans, and target info.
Hackers should also have a tough time following people through the matrix. As Glitch says in the Runner's Companion:
"The saving grace of a total information society is that there’s simply too much data out there—or at least too much data to be sifted in useful time. Yes, a high-end agent will eventually track down what it’s looking for, but, by then, the intel is of no use to anyone. […] The second major factor working to your advantage is data balkanization. What this means is that even if the data is out there, there’s no guarantee a corp can get to it—thanks to those wonderful things, the Business Recognition Accords. […] Hide your digital tracks with excess, contradictory information or pay someone to do it. The next best thing to them not picking up your trail, is giving them a dozen trails to follow." Pg. 23 and 25
This means the hacker has to deal with excess info
and (to a lesser extend) data balkanization. It would be insanely difficult to track a single person's buying and spending habits around, especially when they buy a Horizon CaramelCluster bar from the local Stuffer Shack in Downtown Seattle before jogging over to the Rubber Suit in Everett to buy a few drinks. The target has crossed Snohomish, been captured by thousands of cameras, microphones, cybereyes, and all sorts of random equipment from multiple corporations and individuals. To have access to all that information and chew through it all would take months. Not to mention finding a specific commlink, tracing it, hacking it, and following it and sifting through all the information that it piles up would take ages. Time is of the essence, and doing everything is simply not possible.