I have looked at some post regarding this but nobody seem to have given its answer. For example this post Has the Comment system always required a minimum reputation? talks about this question among some others but nobody seemed to responded to it. So I request the Stack Exchange community to help us out with it.
In the very beginning, the only way to "comment" was to post an answer (which anyone can do); the
@Username became a link to another answer on the page:
animuson♦, in the answer here explains:
This is a very, very old feature before commenting existed and answers were actually used to communicate with other users. The links use a hashtag identifier to link to the answer on the same page, like so:
<a href="#44667">Troels Arvin</a>
I strongly believe the requirement of 50 reputation points to post a comment was there from the very beginning of Stack Overflow, when it emerged from its private beta phase.
As Jeff mentions in Podcast #43, which was posted back in February 2009 when SO was still new:
Joel asks about the rationale behind requiring 50 reputation to leave a comment, but allowing a brand new user to post a question or leave an answer