According to this edit (to what seems like the datasource of the table at m:Wiktionary), there was a drop from 123,316 to 99,846 sometime between 2025-07-09T21:47:27 & 2025-07-10T00:47:25 (both times UTC). [0]

The initSiteStats maintenance script is scheduled to run on Wikimedia wikis at 21:00 each day, and it seems possible that the script won't have reached mywiktionary by the time of the previous edit to that datasource-page at 21:47 (compare T404026#11166945, where - on a different run of the initSiteStats script - it had only reached nlwikibooks at around ~22:40).
The MediaWiki version on mywiktionary had been bumped to 1.45.0-wmf.9 the previous day (SAL); so I guess, if it is something in the software that caused this drop-off in numbers, it seems at least plausible that it may have been something included within -wmf.9 that was then applied on the next run of the initSiteStats script.

[0] (For what it's worth, while looking, I also noticed a slightly-smaller-but-still-noticeable drop from 125,308 to 123,100 in this edit at 2025-06-09T00:47:46.)

Commons Data:Wikipedia_statistics/data.tab is retrieving statistics from the API, at a higher level, so I think A_smart_kitten has identified the likely lower level change in MediaWiki version update... assuming there wasn't a mass deletion of pages on 2025-07-09 .. it's possible the lower number is a bug, or, it corrected a previous bug and was never actually the higher number.

Another possibility is that an edit removed all links from a template and that caused many pages to lose all of their links, removing their "content page" status. (Like most WM wikis, the wiki uses the "link" article-count method. This can be changed to "all" if the community agrees to it. See the documentation of $wgArticleCountMethod for more details.) Because there are so many things that can affect the article count, it's often impossible to tell what caused a drop or rise even after a few hours of significant editing activity. In any case, it looks like the wiki is less than 50 entries away from passing 100K again.

In T407368#11288512, @Dcljr wrote:

Another possibility is that an edit removed all links from a template and that caused many pages to lose all of their links, removing their "content page" status. (Like most WM wikis, the wiki uses the "link" article-count method. This can be changed to "all" if the community agrees to it. See the documentation of $wgArticleCountMethod for more details.) Because there are so many things that can affect the article count, it's often impossible to tell what caused a drop or rise even after a few hours of significant editing activity. In any case, it looks like the wiki is less than 50 entries away from passing 100K again.

Thanks! That's the cause of the dropping of the count. I edited a page from Special:DeadendPages to include a link, then the entries count increase +1.