As is I agree. Having only one specific vulnerability just forces you to get a weapon of that type before you go for it. And it would be horribly unfair to first time players. (Zombies are a bit more easy to understand than molecular disassembler swarms)
Perhaps the 2040 nanoswarms just ain’t that good yet. Say, little movement, so they just act as clouds that do not follow you around. And they only get power in specific regions of a certain lab type. (Say a powered lab, which has its own fusion power generator). As long as you walk around in the swarm something bad happens (or it is just annoying). You could turn off the power but that would kill the lights, and quickly reduce the temperature to sub zero.
So you could use emp/fire whatever to clear away specific tiles of nanoswarms. Or just kill the power, and get a different set of issues.
I think we could come up with better solutions of enemies that cannot be shot. (some sort of active emp field enemy? like the skeleteons but double strength).