If I understand correctly, once anyone of the currency drop-down below the ED then the account will be killed.
You are correct that when an account's balance drops below the existential deposit, its state is removed from the storage to not bloat up the precious on-chain storage. The handling of the remaining balance is up to the runtime configuration, most projects send it to the Treasury or burn it.
You could take a look at Basilisk's take on handling ED in a multi-asset environment which they presented during Sub0 2021 (video). They take multiple factors such as the current price and liquidity into account to determine the ED dynamically. Moreover, they showcase an off-chain duster.
A simple solution would be to map each asset
X1, ..., Xn to a value of an asset
Y hard-coded in the runtime and base your ED on
Y such that the sum of all of your assets' translated values shall not fall below a certain threshold:
sum(Y(X1), ..., Y(Xn)) >= ED.