Even https://meta.wikimedia.org/w/api.php?action=sitematrix does not reports the wikis as closed. That indicates this is not an issue with the extension, it is more with the config.

Not sure how to tag, because the Wikimedia-Site-requests was removed.

It seems the file spcomwiki.yaml under https://gerrit.wikimedia.org/r/plugins/gitiles/operations/mediawiki-config/+/e96f63349b781a46fd60c96fa14609d147f5f56c/wmf-config/config/spcomwiki.yaml needs a closed entry (and some regeneration of other files)
Same for searchcomwiki.yaml under https://gerrit.wikimedia.org/r/plugins/gitiles/operations/mediawiki-config/+/e96f63349b781a46fd60c96fa14609d147f5f56c/wmf-config/config/searchcomwiki.yaml

That the wikis are closed is sometimes say in comments like on T35809 or T55140. On T152882 there are not listed as closed, but should be done when config is changed.

{
    "url": "https://spcom.wikimedia.org",
    "dbname": "spcomwiki",
    "code": "spcom",
    "lang": "spcom",
    "sitename": "Spcom",
    "private": ""
},
{
    "url": "https://searchcom.wikimedia.org",
    "dbname": "searchcomwiki",
    "code": "searchcom",
    "lang": "en",
    "sitename": "Search Committee",
    "private": ""
},

Change 831167 had a related patch set uploaded (by Zabe; author: Zabe):

[operations/mediawiki-config@master] Mark spcomwiki and searchcomwiki as closed

https://gerrit.wikimedia.org/r/831167

Change 831167 merged by jenkins-bot:

[operations/mediawiki-config@master] Mark spcomwiki and searchcomwiki as closed

https://gerrit.wikimedia.org/r/831167

Mentioned in SAL (#wikimedia-operations) [2022-09-12T20:08:54Z] <samtar@deploy1002> Started scap: Backport for [[gerrit:831167|Mark spcomwiki and searchcomwiki as closed (T285685)]]

Mentioned in SAL (#wikimedia-operations) [2022-09-12T20:09:16Z] <samtar@deploy1002> samtar and zabe: Backport for [[gerrit:831167|Mark spcomwiki and searchcomwiki as closed (T285685)]] synced to the testservers: mwdebug1002.eqiad.wmnet, mwdebug2002.codfw.wmnet, mwdebug2001.codfw.wmnet, mwdebug1001.eqiad.wmnet

Mentioned in SAL (#wikimedia-operations) [2022-09-12T20:14:34Z] <samtar@deploy1002> Finished scap: Backport for [[gerrit:831167|Mark spcomwiki and searchcomwiki as closed (T285685)]] (duration: 05m 40s)