Don't worry, kemo. It is most unlikely that someone will break into your car. Pay car parks are generally safe, as are camp sites.
It is NOT dangerous to stop in big cities or towns. Occasionally you hear of somebody who has left a bag on the seat with the door unlocked and a thief has snatched it while the car is at traffic lights, but just be sensible and hide it away, making sure the back doors and trunk are locked.
Again, being sensible, I would not leave anything locked in the trunk that you would really miss ie tickets, valuable items etc. just in case I'm proved wrong! I wouldn't bother with hiding the child's car seat either. Radios are stolen, yes, but I haven't heard of a car seat going before.
Cars also get stolen, but I assume this is true in Slovenia too? If yours is a hire car and looks empty I am certain you won't have a problem. Enjoy your trip and don't worry!