Something of a mystery, isn’t it? Something must have happened to them, because none of them inherited Harrenhal, and instead it reverted back to the crown and then was given to the Lothstons only twenty years later.
One thing that’s noticeable is that while Simon Strong is described as among the “dozen valuable hostages, amongst them Ser Simon and his grandsons” when Daemon captures Harrenhal, he doesn’t show up again when Aemond retakes the castle later. To me, that suggests that Simon et al. died in that period, so that probably puts Aemon and Cole out of the picture.
As to how, I’m going to guess disease as opposed to execution, since I think the latter would be more likely to come up in the text.
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