Ruling Suicune-Riaku--- Suicune-Entei

Weakness is just whatever it says on the card. If a card says x2 weakness, it is always treated as x2 weakness unless a different card effect changes it. An example of a card that can change weakness is Lake Boundary.~Mark
 
The answer to your question is yes, for the following reason:

There were dual-types and dual-W+R as far back as the EX series. The ruling was made that if Pokemon are weak to one or both types of the other Pokemon, both are checked for.

Since LEGEND Suicune-Entei is weak to Water and Electric, x2 is applied twice, and therefore, it does x4 damage. (The same thing happens if double resistance is involved, which would be -60 - due to double-resistances so far being only in Hoenn Pokemon-ex.)
 
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