I have found a workaround that I will be using from now on since Licat has formally stated the automatic update of links to headers will not be implemented.
I have a vault with many long notes in which there are headers and subheaders. I need the Number heading plug-in to help me navigate those notes.
I also use transclusions a lot. If it is just a paragraph I want to transclude, a block reference is sufficient; even for a header with 3-4 paragraphs it is doable to transclude each one separately so as to avoid linking to the header.
But when a header has more than 4 paragraphs it is not doable. So, then I would make my transclusion link to the header and all the paragraphs below until the next header (of equal level or 1 higher) will be shown. That is where the automatic update would be required.
Merging those paragraphs into 1 big block of text to not have to link to the header is not acceptable for readability in Live Preview and Reading mode.
So, here is what can be done: place a <br> between paragraphs, which effectively merges them into 1 block of text, but the <br>, which is not visible when not in focus (at least in my set-up), renders them as separate paras in LP and Reading mode.
You can then link to/transclude that one block of text, and that way a change in the header above will not break the link.