1) I think it's working as intended, since now you have a limited number of interactions instead per day. IMO it was too easy spamming invigorate with the old system anyway.
But maybe losing some energy for every interaction (as it was before) would make more sense, it just needs some balancing gameplay-wise between grindy or too easy.
2) I'm curious about that too, I have the same problem even if I stop right after they orgasm. Seems that as slaves become used to sex, they become horny all the time. The penalty during combat is not that big, so it's not really a problem... not sure if it works as intended or it's part of what needs balancing.
3) Not implemented yet, I guess the tracking stats haven't been updated to the new sex system. However, depending on the sexual acts you do, slaves can develop sex traits like bisexual, homosexual, pervert etc. The "see relatives" screen that should show sister/sons/daughters doesn't seem to work for the slaves either.