TLDR - They got no chips and you get fewer clones.
One of the key features of the clone troopers employed by the Republic, and then the Empire, was that almost all clones had an inhibitor chip in their skulls which forced them to follow commands given to them, for example, Order sixty six.
What made Clone Force 99 unique was that they could operate in combat incredibly effectively without chips. The mutations that they had helped them in combat, but it would also have made the process of cloning more difficult for Kamino.
Let's take a real world example for a moment. Let's take the Ford Model T, one of the most widely produced cars of it's time, and do you know why it was the most widely produced car of all time? It's because it was simple to produce and the process was streamlined on a production line. There were no special bells and whistles, you got a car with four wheels, a seat and an engine. There were no variants which could have stripped down the overall number of cars that could have been built. If a variant was built, then fewer cars could be made as a whole production line would have to be devoted to producing that variant. The variant might be more expensive. You may have to get specised staff and machinery to run the production line. The same principle applies to why the Bad Batch were not cloned, it would have caused production issues and fewer clones would be able to be produced.
To add to this, if the kaminoans did want to produce more clones, they'd have to significantly invest in their infrastructure because, if it's not obvious to anyone watching the films or the clone wars TV series, they don't have much space:
As a sidenote the series about this squad will be coming out at some point in the future and may hint at why the mutations were not made widespread among clones.
