If every chan ran on the same software, then one vulnerability could bring down all chandom. Very few people have even seen the Yotsuba script, so only generic attacks even slow it down. Security is a hassle to do right, and image boards have shown to make people passionate about attacking them. Obscurity works when it's no big deal for everyone to brew their own variants.
Also, who would trade in their pet project to a free lifetime pass to the zoo?