Multi-zone systems are designed to operate anywhere from one to all of the connected indoor units simultaneously - no issues.
The capacity of the full system will be limited by the outdoor unit capacity. If the indoor units are all on at the same time, and their capacities add up to more than the outdoor unit, they will all run a less than full output. This is OK because it's rare for all of the units to be on and require full output at the same time. If this is a concern, you can usually buy a system with a larger outdoor unit.