samples: nvs: set MAIN_STACK_SIZE in prj.conf

- Sets MAIN_STACK_SIZE in prj.conf to 2048 (default is 1024)
  to avoid possible stack overflow
  and adding new .conf files per board.
- Deletes existing board .conf files, as they are not needed anymore.

Signed-off-by: Andrej Butok <andrey.butok@nxp.com>