In most cases, the data is marked as deleted by the app itself -- but because it has not been overwritten, it is still recoverable through forensic tools.
For the record, this is exactly what happens when you "delete" any file. The file system just goes to its little index of disk locations in use, and marks the ones the file's data is sitting in as available. Quick and easy. The data is all still there until the filesystem happens to give those locations away to a new file some day. There's nothing at all special about WhatsApp here. This is just how filesystems work.
Security professionals (eg: when I was working COMSEC jobs for the DoD) know to "zeroize" old data you really want to be non-recoverable. When last I checked, that's a matter of writing patterns of 1's and 0's repeatedly to the disk enough that the old data patterns are no longer recoverable. But typical OS's don't have that as a native operation, and it would be fairly unreasonable (not to mention dangerous) to expect a simple social media phone app to be jumping around the OS to do things like that itself.