If the suffixes aren't meaningful, then a numbering system is strictly better because, as you said, "either way things like which ones are AoE have to be learned by rote."
With suffixes, you first have to create your own internal association for suffixes to some arbitrary classification system, then associate them to spell effects.
With numbers, your native language has already defined this arbitrary classification system for you.
Example:
Assume you are given the spells Carve, Carvo, Carvito, and Carviro and tasked with learning their effects. Assume the suffixes serve no purpose other than to give each spell a unique name.
1) First you have to learn how to distinguish the four spell names from each other.
2) Then you can associate their effects.
If the spells were simply named Carve, Carve 2, Carve 3, and Carve 4, you would skip (1) because the difference between (nothing), 2, 3, and 4 is already well defined in your language to the point that you don't have to think about it.