scripts: kconfig: optimize write_kconfig_filenames

Filter duplicate entries in `kconf.kconfig_filenames` before calling
`os.path.realpath`.

Before (current code), all entries in `kconf.kconfig_filenames` go
through `os.path.realpath`. Including all duplicate entries.

With the proposed change, the duplicate entries are removed before
calling `os.path.realpath`.

Signed-off-by: Guðni Már Gilbert <gudni.m.g@gmail.com>