Lufthansa is notorious for this sort of thing, and it’s a real pain when you book for a specific aircraft type. The A340-300 is indeed rare, but doesn’t quite stir the same emotions as the 747.
BTW., one of Lufthansa’s 747-400s (D-ABVU) just arrived in Shannon for a new coat of paint, so it doesn’t look like they’re going anywhere anytime soon. The -8 will also remain in service and be outfitted with (some form of) Allegris, so I hope you’ll be able to make that upper deck trip another time.