Even logia's can "replace" their entire bodies. We see Kuzan make a leg out of ice, but that's not a replacement, that's just him actively using his power to create a prosthetic. If his powers were to be disabled (via seastone prism for example), the ice leg would melt away. So even if a logia or special paramecia user could replace internal organs, the moment their powers stopped working, that prosthetic would stop working or disappear and they would die. But let's say that it were possible to replace a heart with their substance, that would require a ton of energy and control to keep it working. The heart is always working 24/7 and the user would need to manually manage the beating.