It would be better to discuss it at Wiki, but I can respond here.

> because for some tags, the item described by the tag was not the same
> as the one described by the wikidata item (in my opinion it is better
> to only delete the erroneous links instead of hiding everything)

not really

see 
https://wiki.openstreetmap.org/wiki/Proposed_features/remove_link_to_Wikidata_from_infoboxes#Rationale
for reasons, match quality is only subreason and primary is 
that it is useless for users and if someone really needs it
they can use data items

Data items are often harder to process than infobox parameter
parsing[1], but someone planning to use Wikidata identifier
will need to parse them anyway.

[1] at least in Python and JS and any other language that have wikicode parsing 
library

> therefore if I want to make an application that displays natural=tree genus 
> species
in the user's language, I don't have access to the translation base that is de 
facto
wikidata

(1) you have still access to wikidata genus species entries and it is not
being changed at all

(2) 
https://wiki.openstreetmap.org/w/index.php?title=Tag:natural%3Dtree&diff=2409181&oldid=2386673
 
edit removed dead parameter
|wikidata=Q10884
and linking natural=tree to https://www.wikidata.org/wiki/Q10884 
is not helping at all in something that displays natural=tree genus species

(3) https://wiki.openstreetmap.org/wiki/Item:Q4723 data item still has
link to Q10884 Wikidata entry if for some reason it is needed

(4) please be aware that Wikidata quality, especially for translations
is quite dubious (if someone tried this and deployed this - let me know
so I can report systematically broken description into Polish)


> today I see that a bot is deleting the wikidata, which is not
> the same thing as "hide from the infobox"
>
to quote proposal

"wikidata parameter in infoboxes on wiki pages would become inactive.
Automatic edit removing them should obtain a separate bot approval
(it is not granted by this proposal)."

Bot edits limited to OSM Wiki are not handled by any policy, many people
run smaller or larger bot edits without any approval whatsoever.

In my case I propose them on Talk:Wiki and wait for some time.

This specific edit is also trivial to do in reverse (copy simple entry
from data item into infobox) in unlikely case of people changing their 
mind and wanting to display this tag in infobox.

If someone things that bot policy for wiki with stronger requirements
would be a good idea, feel free to design one.

> what do we gain by breaking the link between
> natural=tree and |wikidata=Q10884 ?
>
See 
https://wiki.openstreetmap.org/wiki/Proposed_features/remove_link_to_Wikidata_from_infoboxes#Rationale
for rationale

> compare osm's translation list with wikidata
> https://wiki.openstreetmap.org/wiki/Item:Q4723
> https://www.wikidata.org/wiki/Q10884
> of course for some, it's even worse, for ex genus=* 30 <> 125
> https://wiki.openstreetmap.org/wiki/Item:Q310
> https://www.wikidata.org/wiki/Q34740
>
Using nearest Wikidata item translations for describing tag
is not useful at all and often will result in highly confusing
and misleading "translations".
But if you really want, you can still do this and you are not affected
by this edits.

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