The purpose of notation is to communicate effectively, and ideally notation should match the thoughts that the writer has and wishes the reader to have. That is, notation should match thought, rather than humans change their thinking to match notation.
When a mathematician (who works often with asymptotics, say in analytic number theory) writes something like O(n), they are not thinking of a set; they are thinking of “some unspecified quantity that is at most a constant times n”. (As de Bruijn illustrates with his L() example: https://shreevatsa.wordpress.com/2014/03/13/big-o-notation-a...) So for example, the sentence
(n + O(log n))^2 = n^2 + O(n log n)
is thought of (by the person writing it) as something like
“when you take n and add a quantity that is at most a constant times log n, and square it, you get n^2 plus at most a constant times n log n”
and not as something like
“the set of functions obtainable by adding the function n ↦ n to a member of the set of functions that map n to at most a constant times log n, and squaring the sum, is a subset of the set of functions obtainable by adding the function n ↦ n^2 to a member of the set of the functions that map n to at most a constant times n log n”,
even if the latter is the fully formal and precise way of articulating it. (Consider “the sky is blue” versus “the sky is a member of the set of all blue things”, where “the set of all blue things” was never a part of the original speaker's thoughts.)
That's one reason for preferring the equals sign.
I think what's happening is that we lack a good theory or notation for talking about unspecified things the way we think of them, and set theory (and associated notation) is the closest thing that anyone's bother to develop. (An unspecified thing is “just” a member of some set. And when someone wants to be fully formal, that works fine enough and in fact the differences disappear. As Thurston says (https://shreevatsa.wordpress.com/2016/03/26/multiple-ways-of...): “Unless great efforts are made to maintain the tone and flavor of the original human insights, the differences start to evaporate as soon as the mental concepts are translated into precise, formal and explicit definitions.”) Using the equals sign here captures the original thought better than ∈ or ⊆.
What's so terrible about a one-way = sign anyway? The problem can't be that it goes “against all mathematical convention”, because using it that way is the mathematical convention for over a century, ever since soon after Bachmann introduced it in 1894. It seems that as people learn more mathematics, they learn to accept a great many things and extensions to notation, but the thought of an asymmetric = sign, used like “is”, is just too much to bear for some people. But everyone who works with asymptotics enough does get used to it and comes to appreciate it, so it can't be that either...