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There's nothing specifically negative in it. How many Web 2.0 companies use blog.domain.com and link to it from the homepage? A lot. The question is whether is a good design. I believe, it's not. Different domain is a different domain. Why dilute the pagerank of the main site by sucking it into the subdomain when you can simply have /bog, /store, etc?

Here is the short experiment I did.

(A) I took a new domain and added it to Google Webmaster Tools. Google Webmaster Tools showed no backlinks.

(B) Next, I took old domain with couple of thousands of links and 301-redirected it to the new one.

(C) Couple of weeks later the links to the old domain started to show in Google Webmaster Tools for the new domain.

Conclusion: 301 redirect essentially transfers the links from one domain to another. If the old domain triggered a link based penalty, next Penguin refresh will penalise the new domain as all the links are essentially transferred via the redirect.

Do not use 301 to get out of penalty. Period.

This splash page is cool for the boss but from the user point if view it is an annoyance. One extra click to get to what I want. Every extra click = lost visitors. It make no sense from both SEO perspective and user experience perspective.

If you want to do something cool like this splash page, go and do a one pager HTML5/CCS3 parallax site.