Why do I have an increase in delete operations on Algolia when using Magento?

To make sure the extension only indexes products which are supposed to be indexed, all the products are processed when performing a reindex without the indexing queue enabled. If a product being processed is disabled, out of stock, or invisible, the delete operation is performed in Algolia, even if the product is not present in the Algolia index at all.

The solution to this problem is to enable the queue. With the queue enabled, only products that meet the requirements are indexed and pushed to Algolia. The indexing queue makes use of atomic reindexing. Because of this, your current index will not be updated: instead, a temporary new index is created. This temporary index will replace your current index when it’s filled with all the correct objects.