We plan to use the same ARTIQ/SINARA crate to control both a trapped ion experiment and some other devices. My colleagues concern that if other devices are connected to the same crate, they will bring noise to the trapped ions. So, my question is: can each I/O card in the crate be grounded independently? or can each I/O card in the same crate be isolated from each other?

In general no. Only some cards are galvanically isolated, others can be using a bal-un.
You can use a DRTIO Satellite system to achieve full isolation of a group of devices from the rest.