I don't think it hurts your website to be submitted to about 500 webdirectories even if they use some software for it.

Most free submissions are in anyway approved month later, so maybe the first 30 or if you are lucky 50 webdirectories they submit your website will approve your listing right away, but the other 450 will take month.

But of course there are good solutions and bad out there, and while I have been looking at the same as you, then I found out that some people have build up networks of directories where they instantly approve without looking at what they approve, so maybe it isn't that good to list your site there, since it will not give you any google credit.