Why is it inadvisable to use the directory?
To begin, it would be nice to have an explanation of what a directory and what a search engine is.
The Directory :
A directory works like a telephone directory except that it is a website. The reference directory of websites is ranked by category. When a site is a directory it is a human being who decides in which category the site will be placed.
The search engine :
The search engine is a robot that visits the website on a regular and automatic basis and references the pages using a specific (and secret) algorithm. In general, you do not need to subscribe to a search engine, it will find your site by itself. For more details on how the search engines work, see the article ''Comment fonctionnent les moteurs de recherche ?'' available on this site.
Now, why is it inadvisable to use the directories ?
Because Google and the other search engines recognize the directories when they visit them and they do not like them at all. Bad directories are often associated with spam indexing. The directories are usually real ''links farms''.
By using such directories, you may end up ''blacklisted'' (to be put on a blacklist) the various search engines and in particular by Google, who is the most important among all. If Google (or other search engines) will place your site on its blacklist, you can say goodbye to traffic in your online store.
However, there are some directories that are ''respectable'' and where it is desirable to register because Google (and other search engines) will visit them and reference the sites present there. Among these good directories, there are Dmoz and Yahoo.com.
About Yahoo.com :
Yahoo.com was in the beginning only a directory, it was only later that it became a search engine. Now, besides being an excellent book, it is the second most used search engine by Internet users (after Google).