Why does pagination stop working when Scalability Pro is enabled?
One of the options included in Scalability Pro is to disable pagination. The reason this option is included is because for very large sites (over 100,000 products) then your archive can become slow simply due to the MySQL code that counts how many products there are and how many pages there are.
If you disable pagination using the option in Scalability Pro then pagination will still work but Scalability Pro pretends there are 10,000 pages instead of calculating how many pages there are.
That means, if you have pagination disabled using the option in Scalability Pro, you should hide the page counts or use an infinite scroll plugin.