With capital ships, you can just press tab to cycle through them, but for ordinary frigates your only approach is to select each on individually. Definitely annoying, but fortunately the TEC scout's timed explosives is the only serious offender in the game.
I'm pretty sure it works that way for all of the ships when you select them as a group--only one activates the ability. Select them as a group and then cycle/subcycle through each one, activating the ability for each ship one by one as you cycle through them.
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