As noted, Time Machine does not support APFS. Per Wikipedia,
Apple_File_System
Unlike versions of HFS+ since Leopard, APFS has no support for
hard links to directories.
[3] This is in line with many other modern file systems, but
Time Machine still relies on them, so APFS is not yet an option for its backup volumes (as of macOS 10.14 Mojave).
Since hard-linking is essential to the functioning of present-day Time Machine, Time Machine's replacement needs to be redesigned from the bottom up. I'm confident the designers of APFS have known this from the beginning and the necessary functionality has been provided for.
While it's true that APFS is optimized for Flash storage/SSD (support for TRIM, for example), most of its benefits apply to spinning HDDs as well.
Many capabilities of APFS seem perfect for Time Machine (snapshots, clones and deltas, whole-disk encryption, increased maximum number of files, crash protection, shared free space on a multi-volume disk...), with one very practical, beneficial result being that backups may require substantially less storage space. I also suspect the crash protection features of APFS (writing updated metadata to a new location, rather than overwriting/replacing the old metadata only after the new has been checksummed/verified) will improve the reliability of Time Machine drives stored on NAS.
I expect that someday we will see a version of Time Machine that is specifically designed to use APFS. I suspect it will be given an all-new name, so it won't be confused with Time Machine. Even after the new Time Machine is released, HFS+ Time Machine will have to be supported for many years.
Due to the use of hard linking, it's not enough to copy a Time Machine archive from an existing HFS+ drive to a new, APFS-formatted drive. The fundamental structure of the Time Machine archive has to be modified. This is likely to be a more complex and time-consuming process than the HFS+ to APFS conversion that takes place when you first upgrade a machine to High Sierra or Mojave. Long after New Time Machine is available, I suspect many people will decide to keep their existing Time Machine archives in HFS+, rather than go through conversion.