I have a Magento 126.96.36.199 running for a year and it's a little bit slow when returning products, since they are a lot. I read about the flat catalog category and flat catalog product options and i want to enable them now. Is it safe to do it now and do i need to do anything else apart from clearing the caches?
Yes it is safe to activate it. But would probably be wise to do some proper testing locally first.
This data is aggregated from the data in the other tables, that means that every time you save a product several
(System > Configuration > Index Management) are refreshed to compile this product data.
So also make sure you have clear the caches and re-index everything.