Or - if its a problem for your campaign to have players who are highly armoure - you could simply tell them not to?

I have read alot of posts on these forums about GM's having trouble with high powered chars due to various game mechanics, and it always leaves me a little puzzled.
Personally in my 25 years of gamemastering (in various systems, but also SR since 1st ed) I never really had a problem with this - I follow a few simple guidelines.
1) Discuss the type of campaign I'm running with my players, mainly, pointing out that while combat is a part of the game, then its a mean to achieve a goal, not a goal in itself.
2) Focus on roleplaying aspects and challenges not involving combat, or involving combat in less direct ways (as some pointed out, there is alot of reasons why heavy armour/weapons is just not always an option)
3) Point out that while killing people is sometimes part of the job, then runners are generally not killers and psychopats who gets a kick out of killing people. Remember its a roleplaying game, not a tactical combat boardgame. Runners generally kill to survive, not to have fun. The sec guards are not evil monsters from a fantasy rpg, they are real people with families, kids, wifes etc.
4) Rules are guidelines, and GM's dosn't have to follow them, this is something I see alot of GM's do "wrong" in my opinion, they try to justify everything they do based on rules - don't, just be fair, its your job as a GM to direct a good story that everyone enjoys, its not your job to spend your time worrying about how to deal with players who abuse (and yes, in my opinion it IS abuse) the rules to max out out their survival potential.
5) Use the world/setting of the game to make players understand that they cannot walk around as highly amoured killing machines without serious consequences. Shadowrunners are meant to be discrete, not make the news regularly due to mass killing sprees or causing wide spread panic from walking down the street with an assault cannon on a gyro-mount. Corps tolerate shadowrunners because its simply to costly to hunt them down (remember, there is no money in revenge) but if a team constantly kills alot of sec guards or causes serious collateral damage on their runs, its not far fetched to imagine a few of the corps getting hit might think its more costly NOT to stop them from repeating it.
Maybe Im just blessed with having players who generally don't go all out except on rare occassions, or maybe they trust me to keep things fair and fun despite my constant "cheating" and dice fudging.
I think it boils down to respecting each other - remember players and gamemasters are not enemies, roleplaying is not about the players vs. the gm - if something troubles you, talk with the players, sort it out - don't resort to silly instant killing chars or sending overpowered opposition against them in a way that defies logic, some runs the opposition won't be a challenge to the players, and thats perfectly fine, they might be able to kill the 10 mundane non-cybered corp sec guards at a facility without blinking, but there IS and SHOULD be other challenges in a run than the combat side of things. Mix it up.