I own two niche directories and I have never understood the restriction of submitting only the homepage. From day one, site owners could submit up to three entries as long as they appeared in three different categories and each submission had a different description. My TOS has something about qualifying for participation in a particular category requiring several pages on that topic and preferably the topic being submitted to is a part of their main navigational menu. I do make exceptions on my craft directory for a site to promote an exceptional product or free project or pattern. (One of my most popular listings is from a travel site about Ireland that has a single craft project to make a travel pouch for stationary.) I'm finding that I have to invite people to submit their sites to additional categories or I add second and third listings on my own. From the beginning I had decided that I wanted to create sites that were resources more so than directories. The last time I looked, I think it was less than 10% of the traffic were submitters on my craft directory and my pet directory might be even lower. I have never had someone try to submit every page. Maybe it's just my niches, but most of my site owners would never classify themselves as professional webmasters - maybe that is a large part why I am seeing such different results.
Agreed. I think most directory scripts have an option to prevent multiple listings from the same URL. Unless I was using a directory with extra link fields I would only add on page per directory. Link Building is obtaining links and making them look natural. No idea how having thousands of links to your homepage looks natural.
There are thousands of deep link directories out there. I've found over the years that more and more directories are allowing them. You just have to know where to look.
Sometimes those interior pages of a site are better than the index page. I will typically allow only one listing per domain though.
Also totally unrelated, but why is it that it seems like 90% of directories look and function like they were created in 1995 by a giraffe?