The assumption that all Dutch text must be following the current official spelling is problematic.
See for example Zijn dat kooplieden of zijn kooplieden dat?, De Nieuwe Taalgids. Jaargang 54 - dbnl where the author clearly made the choice of only putting the acute on the first letter of digraphs: dat zijn zíj níet, de méisjes wél, En díe kerels, dát zijn kóoplieden ; Beschouwingen en opmerkingen door L. van Deyssel., De Nieuwe Gids. Jaargang 48 - dbnl with zíjn, níet, méeste, díe, dóor, zíen, íets; Zes idyllische gedichten, Verzameld werk. Deel 1. Lyrische poëzie, Karel van de Woestijne - dbnl with Zóo, vréemdeling, níet, híj; or Taal van alle tijden door prof. dr. K. Heeroma, Onze Taal. Jaargang 39 - dbnl on the first letter of diphthongs with míjn, bóeken, níet, úitgesproken but óók and géén; or even [Blinkend licht splinterde fijn], Verzen, Herman Gorter - dbnl where the grave is used with dè, zìj; or Klemtoonverschuiving Is het Nederlands een ‘hangmat’-taal?, Onze Taal. Jaargang 61 - dbnl with many more; and so on.
On dbnl.org, there are actually between 4 and 5 times more pages with zíjn and níet, with only the first letters with acute, than pages with zíjn and níét, with two acutes on niet but not zijn. This could mean the majority of zíjn were intentional on dbnl.org, if we’re assuming the níet were. Even when we exclude the pages with niét, with the acute on the second letter
which seems like a typo at best, this is still true. On the web the proportions are different, it looks like 2 times less, but it’s still a significant portion of text where it seems intentional. Ironically officielebekendmakingen.nl has a roughly 50%-50% ratio.
Looking at books, there’s still a significant portion, see Naakt model by C.S. Adama van Scheltema published in 1917 with ìs, wíj, àndere, ónzen; or Twee brieven uit Westerbork by Etty Hillesum published in 1943 with hóe, nóu, Wíj, zíj, zíjn, díe, wàt, jíj.
You can see the authors of The Ethics and Religious Philosophy of Etty Hillesum, published in 2014, using Hillesum’s spelling of wíj. Note that the Brill typeface doesn’t substitute it to look like wíj́ whether it’s tagged as Dutch or not. Maybe it’s onto something.
It’s not just old books or old text. See also ‘Indische is een gevoel’ by Marlene de Vries published in 2009 at Amsterdam University Press with zíjn, díe, níet, líegt, íjskoud, zíel, dóen, júist; or the edition of Joe Speedboat by Tommy Wieringa published in 2008 at De Bezige Bij with rúikt, móest, móet, bedóelde, jíj, híj, míj; Villa Serena by Marion Pauw published in 2009 at Archipel with híj, jíj, níet, schíetschijf; and so on. They follow spelling rules, just not the current official ones.
All these are lost to the readers when shown in a fonts that substitutes íj.
The use of acute as a stress mark on the first two letters of vowels written with multiple letters has only settled as a government sanctioned rule in the 1995-1996 spelling. Jan Renkema mentions the different rules in Schrijfwijzer, 1989, and says they are replaced by the acute rule in later editions. It doesn’t seem to be in the 1954 spelling. Before 1995 the grave was also in the usage for short vowels and and there was some variation in marking stress. Even after 1995, some editors intentionally only put the stress mark on the first letter of what they consider to be diphthongs like níet or of digraphs like vóor.
Unicode had j + combining acute standardized in its encoding in 1992. Dutch spelling rules settled on the current ones for marked stress in 1995-1996. It’s a bother Dutch data was input in Dutch ASCII encodings or ISO 8859 encodings, or with keyboard layouts that didn’t support the j acute. While we know in many cases the users probably want the j acute, certainly when there’s a note like you mention or when they use it, we also know in a significant number of cases they did not want it.
Even today, the Onze Taal spelling recommendations slightly differ from the Taalunie official spelling. They may agree on the stress mark rules but disagree on other topics. Some style guides like the one of the Financieele Dagblad (see Dutch IJ with dots - Page 3 — TypeDrawers) disagree on the stress mark rules. Some users do stick to the pre-1996 rules they learned.
What if tomorrow Taalunie or Onze Taal decide that the marked stress rule can be more tolerant or different?
The user should decide what rules they follow. Unless we know what the user decided, it’s problematic to guess.