It's accessing the XML files that is no longer possible. ODK Collect still exports a ContentProvider that makes instances database queries possible though you won't be able to directly access the database file. There is no explicit documentation about using Collect's content providers but there are Android docs and InstanceProviderAPI should give you the values you need to build queries.
Note that one of the big upcoming improvements to Collect is support for multiple projects. We're not exactly sure how that will interact with the ContentProviders that are exported. It may be that they're only available for the first project created and I encourage you to check in on the documentation once that becomes available.
There are no plans to stop supporting ODK. If you have programming experience and are looking to build complex information management systems, you should check out ODK-X. It's now a completely separate project with a different team.