Please run the 'refreshLinks.php' and 'updateArticleCount.php' scripts (in that order) on the recently created shywiktionary (the Shawiya Wiktionary, T238105).
Based on what I'm seeing on the wiki, it looks like the 'pagelinks' table is not correct/complete.
To be specific:
shywiktionary is currently reporting that 1,128 main-namespace pages are dead-ends (do not link to other pages), but a check of a generous sampling of those pages reveals that almost all of them do actually contain a wikilink provided by a template that specifies the language(s) of each entry.
This "dead-end" data was cached at 21:55, 1 December 2019. I'm not sure if this is local wiki time of UTC+01 or just UTC, but in any case, it was surely after the statistics were initialized, sometime between 5am and noon UTC on 1 December (note that shywiktionary appears for the first time in the 12:01 Dec 1st update of m:Wiktionary/Table).
Now, if you notice (hopefully still true when you read this), the list of dead-end pages starts with "hiḍma" and appears to be in alphabetical order (or Unicode sort-order?), while the list of pages linking to the language template ends with "hizizwin" (also in order). This is clearly not a coincidence.
Also not a coincidence: Special:Statistics claims 903 content pages, which matches the 2,031 main-namespace non-redirects minus the 1,128 purported dead-end pages. But the "true" article count presumably should be very close to 2,000, since almost all main-namespace pages transclude that link-providing template.
Thus, it looks like the wiki is somehow "stuck" with an incomplete 'pagelinks' table, which is adversely affecting WhatLinksHere and the article count of the wiki (among other things, I'm sure). Running the scripts should fix these problems.