Does anybody have any thoughts related to this? Do you try to limit or even close categories? Do you limit the number of regular links overall? How do you maintain any quality on thousands of links? I have a directory where I was getting a submission every day or so, then we were on the top of the new directories list at directorycritic.com over last weekend. We had 200 submissions the first 24 hours and 400 the next, it started to drop down to between 100 to 150, but still a lot of work. An immediate issue is the depth of submissions in certain categories verses all the ones that we want to eventually get links in. So I modified PHPLD to not allow more than 5 links into a category unless it is reciprocal or featured, and have split/expanded several categories to accommodate more links. This helped reduce the number of new submissions down to a manageable number. I can easily raise the cap once we have more breadth but at roughly 700 categories that would still be 3,500 free regular links. I see sites out there with 20,000+ links in them. It doesn't seem like a lot of value being on page 20 for a given category, let alone trying to maintain any quality control over changes in site content, etc. The directory is Koala Dir at http://www.koaladir.com, no live links for me yet!
You shall control the links in your database by reviewing the links and then approve or reject them. You can set a strict rules for accepting submissions. 5 links per page is not enough, and if you are afraid of that, you'd better not run a directory. Or if you have higher pr, you shall change it paid.
Decent directory editors should be re-categorising links at every opportunity, adding new sub categories when there are full categories above them.
A variety of methodologies are used by major directories to keep most topics under control. The simplest one is of course adding sub-topics and secondly the use of alphabars. You will find some even use duplicate topics, for example; SEO Services 1, SEO Services 2, etc.
Your strategy would appear to sacrifice the more popular categories' depth with the thought of increasing less popular categories. Problem with that logic is you could be turning away some truly quality sites in the hopes that some obscure category gets filled first. I don't see anything wrong with limiting the number of free listings in each category but doing so in hopes to get more submissions to another, presumably unrelated category, is unrealistic. I'm also not sure what depth has to do with quality. I'm quite picky what I allow in and one of my categories is growing much faster than the others. It's simply a matter of that type of craft is more popular right now. If I only allow quality sites why would that category growing larger than the rest somehow decrease the overall quality of my directory?
I guess what I am describing is a little bit of a high-bred. I want to keep the size and daily submissions manageable, but don't want to go to a pure paid-directory. Unless your goal is to match DMOZ I don't think quantity of links equals quality. Quality of most directories seems goes down with every 1000 links just because it is that much harder to manage, and the value to the submitted link owners goes down with it. I don't want to have to spend 2 hours a day going through submissions, and I want to have enough time to review what I accept without it being a full-time job. We spent a lot of time reviewing links, and still had a couple slip through still. I put a low cap on just to slow things down, and have been working on some directory management tools to make the process a little easier. So now we are a couple of days behind. I take it the only way other people have tried to limit a directory size is by just becoming paid, which probably cuts the submissions down to hardly anything at all.
It sounds like from your original post that the jump in submissions may be short-term. You might want to wait it out and see if the submission rates continue at their current level. It's a shame that you feel 2 hours a day is too long to invest in submission review. I would suspect many here spend much more time than that.