What are true benefits of being completely brand free from the script (such as phpld) you are using on your directory. I mean of course it may make your directory look more professional but what other benefits come with not be attached to a software. I mean do people even notice or care?
When the branding of any software includes publicly displaying the version, I think it is risky for the site owner. When hackers identify a vulnerability in a particular version, they simply Google for that branding phrase for sites to attack.
Probably no advantage for a young site but I think as your site grows and improves it gets to a point where removing the branding can help establish your site as a more serious concern.
If you build your own software for your directory you have more control over the internal linking structure and content on your pages. By building out good content in your directory you'll have a better chance for the directory to rank in google.
If we want to truly create a valuable directory and want to brand yourself in the market, you need to go for non-branded version of software. The questions is, are you willing to be a brand ambassador of the script that you are using? Or do you want to brand yourself in the market? For people who create YAD this is not a matter at all. However for people who have vision in creating something valuable it does matter a lot.