We limit all things, and 2000 likely seemed like a sane limit at the time the feature was added. It could likely be raised - what is the number that you think makes sense for your community?
That said, that’s an impressive number of blacklisted words! Why do you feel you need more than 2000 blacklisted words, rather than using the flagging system to let your members know the kinds of words that are not allowed on your site?