Those flying root things when you are little Link were really succesful in keeping you on your toes when exploring that large plane. Also the characters and their tunes (like that owl that guides you) were really adding to the atmosphere. Loved the differences in the settings when you travelled through time.
Those flying things used to terrify me because I had no idea what they were. I think the bad graphics give the game a sense of abstraction that really lets the imagination take over at times.
I pictured them right away as some sort of flying meateating (or at least meat hating ) plants as that what came closest to my associations, and I never really thought twice about it (except that I didn't like their look at first.. weird big shape. It was one of my least fav creatures in the games). Of course it was also just perceived and acknowledged as another vague magical evil creature spawned by Ganondorf.