Glad I could help a bit with the Thunder Hawk.
I also just found the same problem with Atlas AS7-D: present for HW Clans General in Late Succession War but not Early Succession War, despite being in Op Klondike table for the Clans. This one is slightly less problematic because I suppose the Late Succession War ones could have been brought back by Wolf's Dragoons from the Inner Sphere. Still, given how much the Clans venerated the Atlas as the mech of DeChavilier and Kerensky, I doubt they would have burned through their stockpiles in the Golden Century to the point where they all lost access to the design entirely for hundreds of years. The Atlas was relatively rare among the Clans, but not extinct. If it did go extinct, then they are literally the worst preservationists of what they claim to venerate of any people in human history. See next point.
Question B: We determined that the Nightstar would not be available to the Clans in later era to reconcile with a passage in the Coventry sourcebook that shows us that a Clan warrior was unable to recognize the 'Mech. For this to happen, we had to allow for extinction in the Homeworlds, limiting the initial number in Clan hands.
Sorry to harp on this a bit more, but how does it make sense for the Clans to forget what a Nightstar looks like? These are the descendants of Kerensky who worshipped everything about the Star League military down to its smallest detail. The Star Captain in the Coventry book who is giving the problematic account is a Jade Falcon, a Clan particularly reverent of the Star League. And the Nightstars didn't just die out with the Star League or the Pentagon Powers. Per the table in Turning Points Widowmaker Absorption, Nightstars were used by Clan Widowmaker, and the Jade Falcons were involved in their trial, specifically the First Falcon Striker Cluster fought Widowmakers on Dagda in 2834 per the scenario on pg. 24.
I mean sure, I guess the Falcons on Coventry tended to be noob warriors, and I guess the Clans could purge their targeting computers of old data for mechs they thought were long dead in order to save some hard drive space, but that doesn't seem like such a great idea in a universe where battleMechs routinely reappear after hundreds of years of not being seen.
Anyway, maybe the great and baffling mass disappearance of the Nightstar from Clan Mech stockpiles and collective memory can be explained in some future product Haha.