For DYNAMITE RAVE, it was due to one of the original vocalists' contracts expiring iirc, though I'm not sure if it was ever confirmed to be specifically JASRAC-related. I wouldn't be surprised if it was, though. For the other ones, considering the classic songs on the current arcade version still have their original vocalists and not the redone versions, I don't think it was contract related (though certainly sounded like it at the time). Maybe Naoki trying to "update" it to the times and failing miserably.
Going back to the Captain Jack thing, despite my long sperging on contracts and all that, I'm sure Konami does have plenty of money to just say fuck it and throw money to get their library even with contractual bullshit, but in all likelihood I don't see it happening given the previous normie/weeb bating reasons + Konami in general being stingy as hell. Plus the nostalgic casuals still go to the other familiar Konami originals without a problem. ngl I don't think I've ever seen anyone IRL be like "eyyo fuck this daikenkai and candy bullshit, where's my captain jack and waka laka????"