> ...doesn't it mean that the companies using the GPL'ed software are violating copyright?
It may be a technical violation. This wouldn't in itself make any difference to anything, however. It would only matter if a court would then award damages to copyright holders as a consequence of the violation. A violation in civil law doesn't mean anything in practice except when damages are awarded (and only changes behaviour when damages could be awarded).
Damages are awarded based on harm done. I think a copyright holder would struggle to show that any harm was done by the defendant, especially as the defendant would have been acting in good faith. Of course this depends on the details of the reason the court ruled the GPL invalid, so it's not really possible to speculate on your hypothetical further.
Because the GPL license is the only thing granting them the rights to use that intellectual property, right?