You asked,
- why are the big braces
\left( only rendered as small regular ones for most of the equations? How can these be rendered as bigger?
The belief that \left( and \right) always create "large" parentheses, irrespective of the material they enclose, is widely held but, alas, wrong. As you've (re-)discovered, if the material enclosed by \left( ... \right) is not tall, then the surrounding "fence symbols" aren't either.
See the posting Is it ever bad to use \left and \right? for in-depth discussions of why \left( ... \right) is not a panacea. In fact, it can be quite wrong at times to use \left( ... \right).
You also asked,
- Using an IEEE two-column layout and some long formulae I want to typeset the long ones over both columns. How can I achieve this?
There are methods to display selected material, including displayed equations, across both columns. For the equation at hand, though, I can't see a good reason for not typesetting it across two lines. This may be achieved by switching from \sqrt{...} notation to [...]^{1/2} notation, switching from an equation environment to a multline environment, and indicating a line break right before the + symbol. Three possible solutions are shown in the following screenshot:
use \Bigl and \Bigr throughout;
use \mleft and \mright to size the round parentheses -- the square brackets are sized via \biggl and \biggr as they span a line break;
use \left and \right to size the round parentheses. Note what many would perceive an excessive amount of whitespace between \sin^2 and (.
Speaking for myself, I'd say that the first solution is the best one.

Note that I've omitted several pairs of curly braces in the equations, e.g., in \cos{y_{lat_2}}.
\documentclass[conference]{IEEEtran}
\usepackage{amsmath} % for "multline" env.
\usepackage{mleftright} % for "\mleft" and "\mright" macros
% utility macro to typeset variable names:
\newcommand{\vn}[1]{\mathit{#1}} % or "\mathrm", or whatever
\begin{document}
\noindent
With \verb+\Bigl+ and \verb+\Bigr+:
\begin{multline} \label{eq:haversine1}
\textnormal{distanceHaversine} = 2r \arcsin \Bigl[
\sin^2 \Bigl(\frac{y_{\vn{lat}_1}-y_{\vn{lat}_2}}{2} \Bigr) \\
+ \cos y_{\vn{lat}_1} \cos y_{\vn{lat}_2} \sin^2
\Bigl(\frac{x_{\vn{long}_1}-x_{\vn{long}_2}}{2} \Bigr) \Bigr]^{1/2}
\end{multline}
\bigskip\noindent
With \verb+\mleft+ and \verb+\mright+:
\begin{multline} \label{eq:haversine2}
\textnormal{distanceHaversine} = 2r \arcsin \biggl[
\sin^2 \mleft(\frac{y_{\vn{lat}_1}-y_{\vn{lat}_2}}{2} \mright) \\
+ \cos y_{\vn{lat}_1} \cos y_{\vn{lat}_2} \sin^2
\mleft(\frac{x_{\vn{long}_1}-x_{\vn{long}_2}}{2} \mright) \biggr]^{1/2}
\end{multline}
\bigskip\noindent
With \verb+\left+ and \verb+\right+:
\begin{multline} \label{eq:haversine3}
\textnormal{distanceHaversine} = 2r \arcsin \biggl[
\sin^2 \left(\frac{y_{\vn{lat}_1}-y_{\vn{lat}_2}}{2} \right) \\
+ \cos y_{\vn{lat}_1} \cos y_{\vn{lat}_2} \sin^2
\left(\frac{x_{\vn{long}_1}-x_{\vn{long}_2}}{2} \right) \biggr]^{1/2}
\end{multline}
\end{document}
Addendum to address the OP's question about allowing a line break in the vinculum of a square-root expression. I initially seemed to remember that this topic had come up before on TeX.SE, but then I couldn't find a prior posting. Anyway, it's not too difficult to introduce a line break by replacing
\sqrt{AAAA BBBB}
with
\sqrt{AAAA} \\ \overline{BBBB}
but the result -- see below -- looks just awful. (I inserted \cdots instructions to help indicate that the square root continued to the next line, but it didn't help much.) I suspect that readers will try to read the full expression as some kind weird fraction and get utterly and hopelessly lost. In short, I wouldn't do it. Use \Bigl[ ... \\ ... \Bigr]^{1/2} notation instead.

\documentclass[conference]{IEEEtran}
\usepackage{amsmath}
\newcommand{\vn}[1]{\mathit{#1}}
\begin{document}
\noindent
With \verb+\Bigl(+ , \verb+\Bigr)+ , and a line break in the vinculum:
\begin{multline} \label{eq:haversine4}
\textnormal{distanceHaversine} = 2r \arcsin \sqrt{\sin^2
\Bigl(\frac{y_{\vn{lat}_1}-y_{\vn{lat}_2}}{2} \Bigr) \cdots} \\[1ex]
\overline{\cdots+\cos y_{\vn{lat}_1} \cos y_{\vn{lat}_2} \sin^2
\Bigl(\frac{x_{\vn{long}_1}-x_{\vn{long}_2}}{2} \Bigr) }
\end{multline}
\end{document}
\big[or\bigg[or a similar thing; 2) it's not easy (see here and you should check if the journal will accept the extra packages. – Rmano Apr 23 '20 at 10:31