I'm GM for a group of runners with several tank characters. High cyberware and high armor. I have a few tricks I pull out to make them sweat.
1: Magic: control actions or a spirit or two. An astral quest maybe?
2: Someone who is packing bigger guns/armor. there is always a bigger fish. Corporate, police, military, a dragon, another runner group etc....
3: Put them in a situation where they cannot have lots of armor/guns. On a boat, in high security areas, a nightclub, in another country, anywhere where they cannot be allowed to bring the heavy gear or they cannot complete the run. Just make sure they don't have the time to collect the gear.
4: Matix: Let them have a matix adventure. you are only as good as your skills and programs.
5: Technology: All cyberware have tags, let it be hacked and the player looses his cyberware momentarily.
6: Numbers: No matter how much armor you have, if you throw a few hundred ghouls at them or animals or drones the numbers will make the runners still feel like they don't have control.
7: Wear and tear: Armor gets worn, have a few runs where they are being hammered with lots of heavy opponents and the armor will me more and more full of holes. (see barrier rating rules). and son enough the armor will fall apart, just make sure the cannot replace it, it takes a few days for a fixer to get them a new one.
This can be done without pulling out the really big enemies. It is fun to let them think out of the box and challenge them to not feel secure. Without going overkill just to harm that one runner who has alot of armor.