Typically you would show prices from ATG even if the search results are provide by Endeca. This can be taken care in the front end. you might have pagination in the front end so that ATG will have to calculate prices only for a pageful of results. Getting the prices from ATG at run time will get you most up to date prices.
The only problem here would that since Endeca might not have latest prices, sorting or filtering will be done on the prices available to Endeca. This should generally be an acceptable scenario to the business.
If you don't like above then you can do something more complex like getting real time prices for all the search results from ATG within Assembler and then using the real time prices to sort on. you will need right skill sets and abundant time to accomplish this.