Not at all but if someone is sending links to
http://www.blah/index.php
and
http://www.blah
Then this can but who really knows affect and generate SPAM points deducted
Definately hurts your count for that page when split in half
dont promote as index.php
promote that as
http://www.domain.com
There is no need to ever call a index.php in a URL
http://www.blah.com/?moo=foo works just the same
index.php is controlled via DirectoryIndex in apache and probably everythign else httpd wise and can be set to auto load before index.html