Just curious, why do you have a SEO Company and you claim to be a "specialist" but don't know the basics?
lol I think link to www.mysite.com. I tend to do this because if you change your architecture and all of a sudden it becomes index.php rather than index.htm any link you've put in place operates as normal. Additionally, there may be some bias towords ranking a front page, that may not be picked up by linking to index.htm. My thoughts anyway.