I'll hate to say it, but when thousands of mods are in danger of being lost forever, you cannot take the luxury of asking each one of the many modders that made them.
Think about how many mods were in danger of being lost forever, if saving them meant to break the permissions of authors, then so be it, it'd be a nightmare to contact all authors, since they archived firefront in general, not just a easily contactable sector.
Of course, if the modder himself comes and asks for the mod rights, they should allow it, but otherwise, the modder might be MIA and his work could be lost forever, and that is something that should be avoided at all costs.
Is it theft? Perhaps, but it's a necessary thing to do for a greater good to be gained, and allow other mods to survive, the modders here are just a small section of those on filefront, but I'd bet that most modders that uploaded something to filefront aren't around anymore, and that means that, if lucky, only a 40% of mods could be kept.