Root Installation vs Security and SEO linking

I've installed and customized my zencart at
http://mydomain.com/cart/.
However, for SEO purposes, I think I'm better off having my store in the root directory:
http://mydomain.com/
because there will be less confusion about the location of my main page especially for getting links to my site and SEO.
(1) Do you agree?
(2) Most importantly, are there any security or other reasons for keeping the cart out of the root directory?

Thanks for any comments or suggestions.

Far as I know, there are no security or other reasons to not have your store in the root, and a lot of reasons to do so.

stevesh:

Far as I know, there are no security or other reasons to not have your store in the root, and a lot of reasons to do so.

Thanks stevesh. I've moved my store to the root. However, you piqued my curiosity when you said: there are "a lot of reasons to do so." What comes to mind as advantages of having it in the root? Thanks.

Search engines assume that pages in and linked directly from the "root" or domain url are in fact more important. As you get deeper they become less important and require a more robust linking strategy to make them pop.

~Melanie

Melanie's is the best reason, but if you have your store in a subdirectory, you'll have to have something in the root to direct visitors to the store, requiring one extra click to get there, and offering one extra opportunity to leave.