ZAP, there's other ways of dealing with a spirit than trying to overpower it with regular ammo. APDS ammo applies to the Hardened armor as well, as would SnS. Capsule rounds filled with KE IV (an insecticide on novacoke) will trigger the spirit's allergy. And I do know groups that always have someone with the longarms or heavy weapons when they expect heavy combat.
In general, though, if you aren't kitted out for bug hunting, and you encounter bugs, you really oughta turn and run, and if you come back at all, do so when you've properly kitted up, with backup.
And Guns, sorry, but that doesn't hold water. If all the fights are 'fair' and brute combat is all the players need to do to advance, then you might as well be playing a FPS with Shadowrun trappings. It isn't about punishing players for not playing 'right'. It is the simple acknowledgement that there are bigger fish than you out there, and going in guns blazing is a stupid, suicidal idea many times. By your logic, if a group decides it would be fun to assassinate the CEOs of all the Big 10 (including S-K), then a GM should make it so that those fights were 'fair'? I call straight bull on that. Yes, in D&D you can kill gods if you're high enough level, but this ain't D&D. It isn't even fantasy. What you're saying goes against not only common sense, but also every example of the setting, and the genre it is set in.