In general citation style is a matter of personal preference that ought to be respected by editors. We don't edit to supplant personal preferences of the original author because otherwise we'd see infinite edit warring.
However, legibility can trump personal preferences, and I think that's relevant here.
Every citation style I know either cites the source naturally in the text—“According to Clarke (2004)”—or has a simple number either bracketed (1) or superscripted2 or both[3]. Now, we're not beholden to APA, Harvard, or any other citation style, but the point is none of them are using long strings of superscripted text without brackets.
Now, this is personal, but taking an example from one of my own posts, I think this is more legible with brackets around the citations:
Later, the Gods would take notice of this experiment. They visited the Mortal World and stabilised it, separating it into seas and land masses, and sprinkling it with life, making it what we know now.[MOP 70] The Primordials eventually discovered this, found their work of art desecrated with Astral life and stability, and wished to return it to the chaotic thing it was before.[MOP 70] Thus the Dawn War was fought between the Gods and Primordials over the fate of the World.[MOP 70] The Gods won, and the Primordials who survived the conflict were imprisoned or scattered far throughout the Elemental Chaos.[TPB 65]
... than without:
Later, the Gods would take notice of this experiment. They visited the Mortal World and stabilised it, separating it into seas and land masses, and sprinkling it with life, making it what we know now.MOP 70 The Primordials eventually discovered this, found their work of art desecrated with Astral life and stability, and wished to return it to the chaotic thing it was before.MOP 70 Thus the Dawn War was fought between the Gods and Primordials over the fate of the World.MOP 70 The Gods won, and the Primordials who survived the conflict were imprisoned or scattered far throughout the Elemental Chaos.TPB 65
Simply because the brackets provide a clear visual break from surrounding text that helps me skip over them if I want to just focus on the text and not its citatinos.
I'm not about to say your citation style is wrong. It was not necessarily correct to replace it, although I can see where the editor was coming from in doing so. However, please consider that using brackets or parentheses around your citations is, I think, going to markedly improve the legibility of your posts.