First of all, thank you for such a detailed feedback and your suggestions. It's the first idle I'm making and the first game I published on itch.io. I expected like 3 people to play it at best, but I got more than a thousand and seeing someone investing so much time to give feedback is amazing and motivates a lot to actually finish the game.
I didn't plan to add any theme(except for math and hypercubes themself) initially but I really like your idea about game becoming more and more uncontrolled/broken by the end. I tried to use upgrades name just as puns, but it could actually narrate an ambiguous story, with narrator changing from helpful guide to just someone who tries to figure things out like the player does.
I agree that later upgrades don't bring much and progress in unlocking new numbers is broken to the end – one upgrade lets you buy too many new numbers at some point. For clarity, I call numbers in the main grid simply Numbers, rhombuses in between them upgrades, and there are only 3 hypercubes(MH, PH, EH).
I think what I will do is to actually use "less is more" approach: I will try making the number grid smaller, leaving 49 numbers and, respectively, 36 upgrades. This will make EH into a purely end-game mechanics, which I hope will make it feel like a finale of it. Also, since I have a lot of 7's around already, it would make sense to 7^2 Numbers.
Also thanks for an idea to keep the x10 button in some way. I didn't think about it, but it would be a nice touch for some active gameplay.
If you don't mind, I'll tag when I do that. I'd really love to hear your feedback again. No pressure of course :)