” For example if there are 2 trades opened for EURUSD and USDJPY…will the daily loss be calculated for one pair individually or for both the trades combined”
The daily loss isn’t calculated you give it a physical number in $$$ and when equity reaches that point the trade is closed and the EA is stopped.
you will have the same $$$ number for all EA’s running so when the number it all the EA’s will be turned off.