It depends on what you mean by second layer. The term is used quite loosely. But I think it means something that is not fully under consensus on the first layer. As far as I know, Omni is (please correct me if I'm wrong) part of Bitcoin's base layer in the sense that all Omni transactions are Bitcoin transactions. Bitcoin nodes execute them after they are included in blocks.

You can store text on Hive in the JSON format. These are stored as transactions on Hive and included in blocks but the Hive nodes do nothing in response to them. But Hive Engine which is a third party service acts upon some of those transactions. The transactions themselves (as just stored text) are part of the base layer but their execution is just the job of a third party - Hive Engine.

If both data and logic are outside the chain, then that stuff does not necessarily qualify as being on the second layer in my opinion.