[Addon Domain Question regarding SEO....]

Yes the Spider will crawl all the links related to the directories and sub directories. What you want is that the spider must not follow the sub sites from you main website. The simple solution for this is robots.txt file which you have already implemented. I think robots.txt file can help you in resolving this issue very easily

[SEO friendly URLS]

As we all know Google bot reads the text better than the any other thing over the Internet. The Text based URLs are crawled by the Google easily and more efficiently as compared to any other URL having a structure of query string in it. But from this we does not mean that the dynamic links do not appear well on the Google. Most of the top ranking websites in the Google have dynamic structure of the URL. However if you are using static URLs you can have keyword optimization with the help of your URLs as well. As you can use Keywords in your URLs as well. This can help in boosting up your SEO Ranking