Will High Sierra also convert secondary drive into APFS during macOS upgrade process? I want to update macOS to High Sierra. This question is for precaution purpose before updating macOS.

I have two drives : SSD-Primary and HDD-Secondary

macOS is installed in SSD and HDD is for backup purpose.

Will High Sierra also convert secondary drive into APFS automatically, when I upgrade macOS to High Sierra installed on primary drive?

Should I disconnect secondary drive before the upgrade?
From the APFS Guide FAQ:


  How do I upgrade to Apple File System?
  
  The macOS High Sierra installer offers nondestructive in-place
  upgrades from HFS+ to APFS for bootable volumes. You can use Disk
  Utility to convert external volumes from HFS+ to APFS format.


(Emphasis mine)

Your secondary HDD is not a bootable volume (assuming it not a clone) so it will not convert unless you do so manually.

That doesn't mean your HDD can't use APFS.


  Can I boot macOS High Sierra from an APFS-formatted hard disk?
  
  Yes. macOS High Sierra supports Apple File System for both bootable
  and data volumes.


You will have to convert the second HDD after-the-fact.

But since you this question is getting info, (like you said) as a precaution, the best advice is to make a full backup before proceeding.