I'm pretty sure when it comes to reprinting comics that Paramount owns it all and can do as they please. It has been speculated they may choose to not include Ninjara because of the adult comics she was in, but that was so long ago I don't think it matters to them much. When it comes to introducing her to new series or for licensing, I think it always came down to the question of "Is it worth it to pay for this character?" and the powers that be decided, "Nah, just replace her with a different, but similar, character." NECA has a history of working with other licensors so if they decided that Ninjara was integral to what they're doing then I think the only thing that would stop them is Paramount if they just plain don't want a TMNT logo on her box. She has since been reintroduced to the IDW universe under her "real" name of Umeko so I don't know if there's truly anything preventing her from being included in this line at this point. Aside from the obvious which is NECA likely losing the license at year end.