@VivMendes
I have been playing a bit with the @tex macro that @fonsp posted a while ago on zulip and was able to recreate automatic equation numbering as well as referencing in other cells of the notebook.
You can find the example notebook here:
Ad here is a gif of the basic functionality:
If you don’t need the equation references as hyperlinks you can skip using the big cell with a lot of javascript code and just use the two function definitions eqref and texeq.
Unfortunately you still need to double escape every backslash for putting the text on the equation environment but that can probably be fixed when PR #1032 is merged into Pluto by using a string literal macro