Should I use an isolated DC-DC converter?
You can, but you don't have to. I would not because for isolation to be of much use, you must isolate all paths to the system. You can't leave direct connections for unpleasantness to go around your isolation. That means that every time your digital logic connects to something you want it isolated from, or connects to something connected to something you want it isolated, you need to isolate those signals too.
For example, if you were concerned enough to use an isolator to protect your logic from noise or other high-power unpleasantness from the motor drivers, you would also have to isolate the signals that interface with all the motor drivers (or use motor drivers where the power-stage and logic stage are isolated onboard the motor driver), as well as signal connections to every other unisolated circuit powered directly off the battery (since the motor drivers are also powered directly off the battery). It can quickly become overwhelming.
You might want to be careful with the LC filter as inputs to your motor driver though...that could cause more problems than it solves. I would have put an LC filter on the digital logic power input instead so you don't have a high-power LC filter in front of the motor drivers.