Yeah... If it were the case that the group should have their Mage able to handle all mystic threats, then the Mage wouldn't need a gun because the Sam would handle all physical threats right? Oh wait, no? Yeah, that's how everyone dies, counting on one person with no back up plan.
It is a major issue of shadowrun that the game runs in three spheres, of which most people can only act in one. It's a problem that is even worse in this edition because they tried so hard to make it difficult to fill multiple rules. You can't play the major from ghost in the shell because both halves of that concept need all the ¥ you can afford as well as different stats and skills. So when the decker eats it, no one can step into his shoes.
Same problem applies to magic. It's probably worse because everyone can at least view the matrix. Mundanes a have nearly zero ways to even check for magical security. You could walk around (if you can be in that area pre run) waiting to feel a vibe or with a pocket full of moss. Granted all that will tell you is if a spirit might be there, which is similar to asking if a run site has security, but getting to know nothing about it.
Not to mention the fact that legwork happens after you accept a job, so your rep gets shafted or you have to buy outside help you didn't intend to, thus making the run a screw job for pay. The entire idea of accepting a job with no legwork done is kinda insane to me. How else would I know how much to charge? Trusting a Johnson to give you the right info (or even know what info you need, he isn't an expert on B&E after all) is equally insane. Maybe it looks like a milk run to some trid watching jackass in a suit, but a real expert knows the entire place is wired with pressure sensors meaning that the job is much more complicated (read: expensive). Likewise, how would a mundane Johnson know about magical security for a run? Is he going to hire a Mage to do a breakdown of it before he hires the group? Not likely.
On a more meta level, how do you know what the biggest dice pool or the most the group will be outnumbered before the run even happens? You can't. So the entire advice for how to calculate average pay is crap. Should a black trench coat group make less because they don't have to shoot it out with an her team? Should the group be able to negotiate on the back end of a run because of increased risk or expenses? "Sorry, you only paid for a shootout with Corp security. Since HTR was tipped off you have to pay our hazard pay rates with a surcharge for change in mission parameters. It's all in the contract you made with us. If you don't pay within two weeks we auction off the pay data to cover expenses. You understand. Tata for now." Click.
Now I'm imagining shadowrunners sending invoices and bills to the Johnson who pays on net 30.
