You actually can edit linker script files manually if you really need to - by turning off the managed linker script mechanism. Generally we recommend that you don't though.
Many things that historically users have hand modified linker scripts can be achieved by, for example, using the memory configuration editor, or the heap & stack editor - which are available through the Project Properties.
With regards to the linkscripts subdirectory, then you are correct, this does not exist in projects by default - as the built in templates are used to create the linker scripts that are autogenerated into the Debug/Release subdirectories created when you do a build. It is only if you have a specific need to change those default templates that you should then create a linkscripts subdirectory, and put the modified version of the specific template you want to change.
This might seem a little strange coming from the KDS mechanism of completely manual linker scripts - but what is provided by MCUXpresso IDE is a system that has evolved, with much customer usage and feedback, over the last 10 years or so. And it means that many users never need to touch the underlying GNU linker scripts with their somewhat esoteric syntax by hand at all.
For more details, please look at the "Memory Configuration and Linker Scripts" chapter of the MCUXpresso IDE User Guide.
Regards,
MCUXpresso IDE Support