Can R help manuals have latex math in them?

Quoting O'Reilly's "R Packages" by Hadley Wickham:

You can use standard LaTeX math (with no extensions). Choose between either inline or block display:

• \eqn{a + b}: Inline equation
• \deqn{a + b}: Display (block) equation

So, using \eqn and \deqn is the recommended and official way.

Sort of. Use something like \eqn{x_1} if you want use the (unprocessed) version of the LaTeX markup in plain-text output (alternately you could say something like \eqn{x_1}{x1}). The "sort of" part is that I'm not sure offhand for which particular output formats the LaTeX processing will be done -- for example, I'm guessing that the HTML-formatted version of output you would see in (e.g.) an RStudio documentation pane would not respect this markup. (The LaTeX markup definitely will be used in the PDF versions of the manual, which I almost never look at ...)

I'm going to go ahead and quote from the Mathematics section of Writing R Extensions ...

Mathematical formulae should be set beautifully for printed documentation yet we still want something useful for text and HTML online help. To this end, the two commands \eqn{latex}{ascii} and \deqn{latex}{ascii} are used. Whereas \eqn is used for “inline” formulae (corresponding to TeX’s $…$), \deqn gives “displayed equations” (as in LaTeX’s displaymath environment, or TeX’s $$…$$). Both arguments are treated as ‘verbatim’ text.

Both commands can also be used as \eqn{latexascii} (only one argument) which then is used for both latex and ascii. No whitespace is allowed between command and the first argument, nor between the first and second arguments.

The following example is from Poisson.Rd:

\deqn{p(x) = \frac{\lambda^x e^{-\lambda}}{x!}}{%

p(x) = \lambda^x exp(-\lambda)/x!} for \eqn{x = 0, 1, 2, \ldots}.

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As of 2020-05-08, the mathjaxr package, by Wolfgang Viechtbauer, is on CRAN. It

Provides 'MathJax' and macros to enable its use within Rd files for rendering equations in the HTML help files.

From the README file:

[After installing the package, editing the package DESCRIPTION file appropriately, and adding \loadmathjax{} to the Rd file ... a]n inline equation can then be added with the \mjeqn{latex}{ascii} macro, with the LaTeX commands for the equation given between the first set of curly brackets (which will be rendered in the HTML and PDF help pages) and the plain-text version of the equation given between the second set of curly brackets (which will be shown in the plain text help). With the \mjdeqn{latex}{ascii} macro, one can add ‘displayed equations’ (as in LaTeX’s displaymath environment).