PAD could've done more with the Tholians since there was supposed to be a war involving them occurring in his New Frontier books.
Specifically, they back Selelvia in a short and pointless war against the Federation, some time in 2377 (after Vulcan's Soul
and before Homecoming
, around the time of the last SCE stories). Acknowledged as pointless in-universe, I hasten to add. I have no idea what NF would have done with this had it shown the conflict, but I think it works well enough as part of the "mainstream" novel 'verse (it's mentioned in Articles of the Federation,
so it did happen).
Presumably Selelvia doesn't know when it's beaten and tries to soothe its injured pride by launching missiles and hiring Orion mercenaries, and the Tholians back them (and give them enough power to actually cause real trouble, perhaps?) because, hey, someone's kicking the Federation, this is too good to pass up.
Tying it in to the wider novel 'verse continuity, I note that The Genesis Wave
occurred in early 2377 (shortly before Vulcan's Soul
). We might speculate that the Tholians were particularly angry at the UFP for having allowed the legacy of the Shedai to cause havoc, and so were feeling even more bitter towards the Federation than usual?