1) Only if your motors have resonance issues at lower speeds. Sometimes faster acceleration can help with resonance. But, if resonance is not an issue, then no, lowering the accel shouldn't cause any problems. However, faster acceleration is usually desirable.
2) Probably not stalls, but possibly. Your steper driver manufacturer should have a minimum recommended pulse width that the drive needs to work properly.
3) Dir low active will just reverse motor direction when changed. Step low active can result in lost steps if not set properly. Again, the driver manufacturer should specify the correct setting.