I have a 3.5 inch Seagate HDD which I have been repeatedly installing and removing from the drive bay. As such, there are some scuff marks (scratches) on the HDD's sides and the front. Will this affect its lifespan and reliability?
Without an image, its hard to tell, but harddisks are very resilient. Of course, dropping them is a different story, but with the wear you describe, no, scratches won't affect its functionality at all. The internal components are away from the casing and are hold in place by screws and thick metal.
Unless the harddisk is bent in a serious way, or it has fallen, you will be fine.
The only thing that scratches really can do is damage the warranty seal and make it void the warranty.