I think the "Threat" mechanic has been disabled for the time being. Maybe it will be reimplemented at some point.I've played SU for about 560 game time days with virtually no response from the Justice League. Hell, . . . that gives Joker a chance to escape from Arkham at least 2 or 3 times without Harley making appearances. For being the "Worlds' Greatest Defective", Batman doesn't have a clue, especially with Batgirl not running night patrols for year and a half. You would also think that the Crime Syndicate being as paranoid as they are would start to wonder what happened to one of their most powerful members, . . . .
Joker hasn't shown up to annoy Luthor for a long time, . . . I still wanna see what happens when Joker is confronted with 2 Harleys, . . .
Knowing Joker, he's probably forgotten all abot Harley while he's working on his latest scheme. Or after excaping from Arkham, figures she's gotten herself into some other trouble and, let's face it, Joker doesn't care for Harley anywhere near as much as she cares about him so, Joker's written her off. Also, Lex has stated that the mind controlled girls will only show up while they are sleeping, so unless Batgirl falls asleep during her patrols, she's still doing them.
As for The Crime Syndicate looking for Superwoman, this game might take place after they have been defeated so everybody in that alternate univerese just thinks she escaped from jail.
I think the only thing Lex has to worry about at this point is Alternate Harley's friends.