The dementors serve at least three purposes in Azkaban: they drain the magic from prisoners to render them helpless, they notify the guards when prisoners escape, and they chase down and incapacitate escaped prisoners and intruders. If Harry destroys 90% of the dementors, there probably won't be enough left for the first or third purposes. That would make Azkaban much less secure, and the perception of Azkaban's security would go down if there are hardly any dementors since the dementors are what make it infallible. Even just demonstrating that Dementors CAN be destroyed would probably force them to completely remake Azkaban to not depend on the dementors.