SharePoint Server 2016 Hybrid search gives empty results in on premises

If you can find your on-premises content in the SharePoint Online index, the crawl process is probably working just fine.

In order to get searches working in your on-premises search center, you need to setup a result source pointing to SharePoint Online:

https://technet.microsoft.com/en-us/library/mt668455(v=office.16).aspx

After you have created the result source, be sure to set it as the default in order to get your search queries being sent to SharePoint Online.

You also mention you have multiple search service applications - you don't need this to have hybrid search working, although there might be another reason you have multiple ones. In any case, make sure you have the right search service application (the hybrid one) connected to your web application through a service application proxy group. If you're not connected to the right search service application you of course won't get any results from SharePoint Online either.

Running the hybrid configuration wizard is not needed to get hybrid search working, but it won't hurt your setup either.