Parentheses disappear in Equation mode in ACM class

You get warnings in your log file:

Missing character: There is no <B9> in font lmsy9!
Missing character: There is no <B9> in font lmsy9!
Missing character: There is no <BA> in font lmsy9!
Missing character: There is no <B9> in font lmsy9!
Missing character: There is no <BA> in font lmsy9!
Missing character: There is no <B9> in font lmsy9!
Missing character: There is no <BA> in font lmsy9!

(the actual output may differ in how it displays <B9> and <BA>).

The problem is that the acmart document class loads newtxmath with the option libertine, which assigns different mathcodes to ( and ), precisely "42B9 for ) and 52BA for ) and this explains the “missing character” warnings.

The standard mathcodes are, respectively, "4028 and "5029. You might get away with such problems by redefining the mathcodes:

\DeclareMathDelimiter{(}{\mathopen} {operators}{"28}{largesymbols}{"00}
\DeclareMathDelimiter{)}{\mathclose}{operators}{"29}{largesymbols}{"01}

Here's the complete code:

\documentclass[sigconf, anonymous=true]{acmart}
\usepackage{lmodern}

\DeclareMathDelimiter{(}{\mathopen} {operators}{"28}{largesymbols}{"00}
\DeclareMathDelimiter{)}{\mathclose}{operators}{"29}{largesymbols}{"01}

\begin{document}

\title[XYZ]{XYZ}

\maketitle
\begin{equation}
Output = AES_{K}(0),AES_{K}(1),AES_{K}(2),...
\end{equation}

\bibliographystyle{ACM-Reference-Format}
\bibliography{PRNGbib}

\end{document}

Note, however, that it's possible to have other mismatches between the defined mathcodes and those expected by lmodern. Also some parts of the document may use Libertine nonetheless.

Final advice: the acmart class has been carefully written to comply with the standards of ACM and affiliate conferences. Changing the appearance of the output by loading different fonts than what's defined in the class should not be done and it could be a good reason for rejection of a submission.