The Product Variants count displayed on the Algolia Shopify plugin is populated by performing an empty search query on your products index.
If your distinct parameter for deduplication has been activated, the attribute that's set as an attributeForDistinct will limit the number of returned records that contain the same value for that attribute. Upon performing an empty search query, the number of returned results can be far lower than the actual number of records after deduplication.
To prevent this issue, you may enable the "Show products instead of variants" setting via the Algolia Shopify plugin instead of configuring the distinct parameter directly on Algolia Dashboard.