Lol. I’m sorry to say it, but yeah, Hisako’s whole gameplan kind of revolves around that feeling of rock-paper-scissors, except that she’s trying to make you feel like she’s always somehow got the exact move to beat you out. 
Let’s address a few of the items in turn though.
First up, I think that playing against Hisako more consistently or taking her into training will bring your breaker game up to par. She’s got a bit of a reputation as being hard to break, but once you get used to her she’s not really all that different - and for the record you actually broke almost every delayed double that I did. I think you might be further along on this than you think.
I feel like this one is just kind of the games we play. Hisako’s really easy to bully on wakeup, but there are ways to go about the bullying. You actually tagged me a lot on my wakeup, much to my chagrin. The only things I’d add would be to maybe try incorporating neutral jumps on Hisako’s wakeup (though not entirely sure that’s ideal with how floaty Thunder’s jump is 
) and to try and vary your spacings a bit more. Where you’re standing will tell a lot of times which button you want to go for - max range is either overhead or command grab, close-mid is your cr.MK, and point blank is your st.LK. Play around with those spacings a bit and you’ll probably be able to bait out some incorrect counters.
And also, just accept that you’re fighting Hisako and will get countered at some point while pressuring me on wakeup. Whenever I managed to counter you on my wakeup, you’d instinctively go to a command grab on your next oki opportunity - don’t let Hisako subtly condition you in that manner.
Lol. Pretty sure I’m the one who told you to “just hold up” - it’s actually pretty solid advice against 90% of the Hisako’s you’ll run into online. While you’re correct that it isn’t hard to punish jump-outs once you’ve worked on it a bit, most Hisako’s haven’t worked on it, and will only know how to hit you with the command grab reset. More to the point, you don’t really have a choice in the matter - if you never jump out or otherwise avoid one of her command grab resets, then you’ll just keep getting tagged by them. Anyone I’ve played on these forums can probably attest to that - if you don’t avoid them, then I will just keep doing them. I think that’s true for most Hisako’s.
What you can do though, is actually backdash out of her resets. Appropriately mashed backdashes will avoid both influence resets and the cr.MK anti-jump reset. I don’t generally recommend that because I think it’s harder to pull off (at least on stick), and if your timing is off you’ll get tagged by whichever one I happened to do. If you can mash DP fast enough, that will also beat any reset attempts.
The thing is though, is that there are still counters to each of these items as well. If I know you DP while I’m comboing, maybe I’ll drop it into a counter instead (that one really puts someone on tilt). If I know you mash backdash, then I can just drop the combo into a raw ORZ. Or maybe, because you’re now super focused on avoiding all these different resets, I’ll instead just do super traditional combos into HKD ender to keep you in the vortex. After all, if you’re mashing DP you’re not breaking, and if you’re mashing backdash then your attention is slightly divided.
And that’s the rub. The resets aren’t just for damage - they also serve as a very important distraction to all the damage I’m doing within the traditional combo system. Essentially, good Hisako play (I think anyway) is a lot about just putting so many options out there for the opponent to think about that they’re a little slow on some of the fairly basic things that are happening around them. My advice is to kind of approach some of that stuff the way you approach Spinal’s mixups - make your guess and make your peace with it, and then deal with the aftereffects whatever they are. Sometimes you’ll get it right and sometimes you won’t, but keep playing your game.
And I think that’s probably accurate. But one of the ways I think opponents should regard this dynamic (which exists in every MU, but Hisako relies on), is that all that really means is that I guess better than you do. There are reasons for that, and there’s a lot of conditioning on my part that goes into making those guesses, but at the end of the day that’s all they are. Guesses. Hisako relies on guesses - on being able to dictate the pace of the match such that she has a decent idea at any given moment in time what the opponent wants to go for.
You can’t get away from that when fighting her, but you can use it against her. Disrespect her. Jump in with obvious telegraphed jump-ins and push buttons. Meaty her with the exact same button she just got done countering. Do all kinds of ridiculous nonsense that will have me saying “I don’t believe he just went for that”. If you play at a Hisako’s pace you will lose - sometimes you just have to kind of toss out absolute nonsense that makes me truly have to guess what it is you’re going to do next.
Sorry for rambling on so long 
Hope that helps!