Remember that police certificates are only one part of the story. They only tell that someone has been caught and convicted of a crime. In countries with corruption there are many people who committed crimes and got away with them... It also only tells of the past, and not about the future, nor what connections or activities people may be involved with.
When the authorities are not sure of a person the CSIS will evaluate them. This can take time, especially when a lot of the information about them is in a country where information is spotty and unreliable. It will be hard to do much about this, because nobody will agree to let suspect applicants in without a CSIS check.

And it's not until after the check has been done that they can be sure if the person is dangerous or not, so it has to be done in some cases.
Obviously in a perfect world applications would be processed and given a decision on the same day they are received, and nobody would ever submit false or frivolous applications, but we do not live in a perfect world...