Where are these max links/day numbers coming from? I'd imagine this only matters when they get indexed right? So doing 1000 links one day, 0 the next few would be alright if we assume google can only index maybe 100-200/day? No way they can find every single one of them right?
Yes, this "too many links" per day is exaggerated. Even if you submit to 500 directories in one day it will take different time for them to approve your link and then different times when Google will actually find that link. You can test that with Google Alerts and you'll see when Google comes across your link (name, URL, ...).
If you get thousands of links from directories it won't help. Thousands of natural links will be fine. I built 50,000 links in about 10 weeks to blogstorm.co.uk and the site ranks better than ever.
Mind I ask how you built 50k? I have maybe 1.2k on yahoo in about 2 weeks, but 0 reported by google. this link building business is tough nevermind, found it in your sig