Yes, the fusion drive would be converted to APFS. Beginning with Mojave, all system drives will be formatted with APFS, regardless of whether they are flash-based or platter-based. The Fusion drive, as you may know, combines those two elements into one unit. Using the drive utility you need to check and see if your backup drive has been converted to APFS. If it is not APFS I'm not at all sure it can be used to restore a system. Perhaps others with more in depth knowledge of how external backup storage works in the Apple world can give you a more definitive answer.
I do know that a Time Machine backup storage drive cannot be used to restore a system that has a later OS in place than was in use when Time Machine was first setup. To be safe, I would reformat the Time Machine backup drive (assuming here that you are using TM) in APFS and setup TM anew.