This will only work for bookdown::pdf_book format, but in the file preamble.tex, you can override the \eqref macro to use \Cref from the cleveref LaTex package, and then just specify the format accordingly. My preamble.tex looks like:
\usepackage{booktabs}
\usepackage{cleveref}
\renewcommand{\eqref}{\Cref}
\Crefformat{equation}{#2#1#3}
In the Rmarkdown document, the reference is the same: Equation \@ref(eq:"label")
In any other output format, the equation label will still be in parentheses.