I guess this problem would apply to any registers that both your ISR and main program modify using &= or |= operations that don't get converted into SBI or CBI.
I would assume so, unless they are running with interrupts off. I am not yet very familiar with the Arduino environment, but is it possible that the environment already has ISRs that interfere with ports in unsafe ways like this? The PWM code comes immediately to mind. Could digitalWrite() interfere with PWM pins that it should not? If so, a programmer need not even write an ISR for this to be a potential problem. I realize that it would probably go unnoticed since the PWM might just skip a cycle, but if the PWM were being used for something important, it might matter.
I wonder if there are other main Arduino envrionment potential victims where data loss/corruption could actually ensue, the SoftwareSerial library comes to mind, although it probably does not run in an ISR. The ISR seems to be the routine that will lose out, not the main program right? I would still think that it would be nice if digitalWrite() did not interfere with another digitalWrite() even if one of them is in an ISR.