I thought to change my earlier choice of a Correct Answer, as whilst it did solve a particular case, and is the correct way to manually add new includes into a project, it actually did not solve the problem related to those two missing links as I found another scenario that is related.
This case is rather strange and it took a good while to figure out.
If I create a new project with say an FRDM-KL25Z board or others and then create a new project with an FRDM-KW41Z board then all includes for all project are resolved and everything links ok.
If I then exit from MCUXpresso and then reopen the IDE and go to say my new FRDM-KW41Z project or any of the other projects I had created) it shows the following (links are now missing):

To confirm this, I can then choose Project... C/C++ Index... Search for Unresolved Includes, and this menu option will then pick up <stdio.h> for you.
This occurs for both c and c++ projects.