Not sure about "subfolders way" as all Versioning options use subfolders. The difference is where the ($SBV$) subfolders are.
It might also be useful to quote your version number (x.x.x.x)...
Standard settings to delete files not on Source will not trigger Warnings about 'folder not empty', but settings to delete empty folders might
Modify > Expert > Copy/Delete > Folders
Modify > Expert > Decisions-Files > Folders
Note that these are Warnings, not Errors and will not set the Result as Failed. If you want to use Versioning, you need to live with them.
Bear in mind that Versioning on Destination will capture any file that the 'if not on Source setting' deletes (for however long you set it to keep them). We just treat deletions as fairly drastic 'changes'...
Hidden $SBV$ folders are not deleted if they contain files (which presumably they do, and presumably you want them to, or you would not have set that). Note that much of the standard logic in a profile will ignore such $SBV$ folders (self-deletion of empty folders is carried out by the Versioning logic itself: they are created as needed and deleted when not)
In answer to your last question, yes ('old' files on Dest that are no longer on Source will likely be deleted immediately/next run). This is because there is no attribute on either side* to say when the Source files were deleted, so the LastModified attribute on Destination is the only indication there is about 'likely relevance'). Bear in mind that if using Versioning, they may well be turned into a Version (not deleted outright), as mentioned above.
* there is not even a file on Source, by definition...
It might also be useful to quote your version number (x.x.x.x)...
Standard settings to delete files not on Source will not trigger Warnings about 'folder not empty', but settings to delete empty folders might
Modify > Expert > Copy/Delete > Folders
Modify > Expert > Decisions-Files > Folders
Note that these are Warnings, not Errors and will not set the Result as Failed. If you want to use Versioning, you need to live with them.
Bear in mind that Versioning on Destination will capture any file that the 'if not on Source setting' deletes (for however long you set it to keep them). We just treat deletions as fairly drastic 'changes'...
Hidden $SBV$ folders are not deleted if they contain files (which presumably they do, and presumably you want them to, or you would not have set that). Note that much of the standard logic in a profile will ignore such $SBV$ folders (self-deletion of empty folders is carried out by the Versioning logic itself: they are created as needed and deleted when not)
In answer to your last question, yes ('old' files on Dest that are no longer on Source will likely be deleted immediately/next run). This is because there is no attribute on either side* to say when the Source files were deleted, so the LastModified attribute on Destination is the only indication there is about 'likely relevance'). Bear in mind that if using Versioning, they may well be turned into a Version (not deleted outright), as mentioned above.
* there is not even a file on Source, by definition...