It will feel hot because it is not 100% efficient in producing light from the electrical power, and the rest inevitably ends up as heat. I'd expect that some of the heat from the cpu, gps receiver and radio will also emerge through the screen, and I assume you are charging it while using it (unless you have a very large battery) which also generates heat. So the phone, including the screen, feeling hot after 9 hours use as a sat nav is not at all surprising.
Will it do any harm? Well if it gets too hot the battery longevity will be reduced, but the S4 has a replaceable battery so that's not the end of the world. OLED screens do have a finite lifetime, but I don't have any real numbers on how long you can expect them to last. If there are parts of the image which are unchanging you may find that those bits of the screen degrade quicker (or slower, for black images) than the rest, which could eventually leave a faint after-image ("burn in"), but generally the main effect is a gradual colour shift (the different colour LEDs have different lifetimes, and if there is a dominant colour in the display you will be using some LEDs more than others. My last AMOLED phone had developed a greenish tinge after 3 years, but as it happened gradually I didn't notice it most of the time). But you'd be better off asking in the S4 forum whether anyone has experienced these effects.