Update:
Well, we decided to go ahead and take off that second layer of tile. And, we found that there are 2 more cracks across the floor in exactly the same spots as the floor joists. We’re afraid that the subfloor is warped — or something is happening that we can’t see. My husband thinks it all needs to come out and put a new subfloor in.
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That's too bad. Judging by age of house, that's a mud-set floor, so you'll have a lot of demo to do (and sub-floor to build up).

Well, since I wrote that update ( a few hours ago, he is changing his mind. Thinking about just covering tile with hardiboard —because we think it is a mudset floor. We’re hoping that we can smooth out the cracks and divots with thinset and lay the board with seams perpendicular to the joists (if that makes sense.) Does that sound sensible to you? We knew we would get into some dilemmas. Old houses have a lot of quirks with a lot of people over the years doing some crazy stuff.

I doubt that's an approved method but it might work, considering the size of tile you're using. You'll have to figure out what kind a fastener for the board (and you'll need a lot of them), as the mortar bed in thick-set installation is usually fairly soft. You'll be higher up on the tub and other stuff. You may have to add an extension to the toilet flange.

No, it does not sound sensible. You should remove it and fix the structural issue.

After doing some research... what about using Ditra over the oldest tile after filling/leveling any cracks with thinset mortor? We plan to use small porcelain pennytile. The Ditra is 1/8" and says it "uncouples' the surface from the substrate. https://www.homedepot.com/p/Schluter-Systems-Ditra-54-sq-ft-3-ft-3-in-x-16-ft-5-in-x-1-8-in-Thick-Uncoupling-Membrane-DITRA5M/100143471

UPDATE— nevermind about this. pennytile doesn't work on Ditra. not enough support for tiny tiles.

"Don't do it. I've seen hexes set over Ditra, with the flat trowel the day before method. The result? Lots of busted grout joints, and hollow sounding tiles. Seen the same with 1x1 and 2x2's also."

Middle of the night research doesn't pan out. This is going to be much harder than the powder room unfortunately. We demo'd that room down to the studs but the substrate was just plywood.

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You are avoiding the fix. It must all come out. Lath and all. When you get down to the Car decking share some pics and we will help you do it correctly .

Yes thank you @Mint Tile LLC — in the last hour, we came to our senses. We're going to call someone to do the rest of the demo of the floor, see what's going on, repair and get the subfloor ready for me to do the tiling. That way we know it's done right and there are no structural issues. I'm just hoping that we can get someone in here before Christmas. At least we haven't removed any fixtures and everything is still hooked up as this is our one shower/bath for us and our teens.

It all needs to come out. Thats a tremendous amount of weight, that was on that floor before you did the top demo. Dont add more weight to it, when its already stressed. Remove it all, and do it right.