If I have more than one copy of Iron Fleet Raiders in play, can an opponent discard a single card to lower the str of both characters since the name is the same? I am guessing no but don't want to have it come back and bite me in the arse...

No. Anytime a card uses its own title, it is only referring to THAT instance of the card, not any other card that may have the same name. So if you have 2 copies of IFR in play, and someone discards to reduce the strength, they are choosing to execute the ability of ONE of the raiders, which does not affect the other one.

In a corollary to that, you cannot pay the cost of two separate abilities with a single action. For example, if you have one Dragon Thief in your hand and one Flame-Kissed, you cannot kneel the same 2 influence to play both cards.