No, I'm sure they still have some sort of professional military among their cities on Vekta. After all, tensions are constantly high, and the Helghast haven't forgotten what the ISA did to them. We'll be seeing them soon.
No but it's true they are citizen soldiers-probably. Apperently Vektan offered the Helghast survivors sanctuary at Vektan. So it stands to reason why they used I.S.A tech, and that they don't have an actual military.