I've had to combat spam quite a few times and find the quickest, simplest way to do it is to rename 'add.cgi' to something slightly different, update Links.pm with the new name and rebuild!
(add.cgi is ONLY referenced from my category pages so I don't have to worry about updating static pages on my site).
Although this can seem like a pain to administer, if you change it on a regular basis it helps to stop any of the submission programs getting a firm hold of your add script location and after a while they'll stop trying.
You could also have a look around and bookmark the various 'Submission' software packages people are selling where they list the SE's and DIR's their software submits to - look to see if you're listed. If they're showing your site send a polite email asking them to add a link to your 'general' submission page that describes how people should proceed, as opposed to the add script itself.
You could also look at your
validate table to see if all the spam links are coming in to a specific category or selection of categories, if so, someone may have got the Category ID's and be using them to spoof submissions. If that's the case you can remove the categories (delete that/those specific ID's), add them back in (create new ID's) and then move all the valid links back into their respective places.
As you can see, there's a variety of things you can do, but ultimately you're not going to stop people
trying to spam you so you've just got to arm yourself with a few tactics for dealing with them and be swift and ruthless when you find them
Hope this helps.
All the best
Shaun