Every shutdown in recent memory, employees were given back pay. I think the ones that are negatively impacted are contractors working in government agencies but not actual GS employees.
On the contract that I am on at NASA, we got back pay the last time the government shut down. But we had it specifically written into our contract that if government employees were sent home for a facility closure, we would be reimbursed.
Sadly, our new contract does not have that written in this time. We have to use vacation days to make up for the missed work days.