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I am at the beginning of my career, but I already participated in several conferences and published 1 paper (and a reply) as the main author, and co-authored a revision with many other authors. In total, I currently have 11 citations.

In my first publication, I used the last name (A) that is very common and which I don't identify with. In the review, I started using another last name (B) which is less common but still not very unique. I came now to the realization that I can use my mother's surname (C), which is very unique, pronounceable, and have other nice interesting features as beginning with the letter 'a'.

Currently, I am about to finish and defend my MSc dissertation and there are probably more publications coming along the way. Is it too late for me?

For reference, A yields > 4million results in google Scholar, B yields ~ 1million, and C have less than 100 entries.

RMS
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If your full name, or initials with last name is common in your field, there might be some inconvenience. But otherwise I doubt that uniqueness has much value. I share a full name with another prominent researcher but in an entirely different field. It is sort of funny when the search turns up both of us, but it is obvious that we are different people.

Consistency, on the other hand is very important, though at the very beginning, the earliest papers may not be so important to the overall career trajectory. But, by the time you finish a doctorate you should establish a name that you can live with throughout your career. Hopefully your earliest work won't be your best work over a long career and a few exceptions won't be an issue.

A personal web site (or one hosted by a university) can be useful in pointing to your work, even if done under different names initially.

For the record, it should be noted that some people publish under a pseudonym to maintain both uniqueness and consistency.

Buffy
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