The difference between relational databases and JSON databases lies in their ability to handle arrays. JSON databases, such as Couchbase and MongoDB, offer flexibility in terms of array type, size, depth, and elements, making them suitable for operational databases. However, this flexibility comes with limitations, including the inability to index multiple array keys simultaneously and the need for separate index entries for each element. To overcome these limitations, JSON databases use inverted indexes, which are ideal for indexing and searching array values, especially when they have duplicates. The upcoming Couchbase 6.6 release will support using FTS indexes for processing complex array predicates, improving the TCO of array handling and enabling developers to use arrays as needed without limitations.